DOUBLE CRITICAL ERROR AGAIN WITH PRIMARY CLUSTER

[Hundred56]

Hello!

I encountered some errors when using dRep.
The version of dRep that I used was:

Check_dependencies:

I originally intended to perform redundancy removal on 38,530 viral genomes, but upon checking the output folder "dereplicated_genomes", I found that there were 35,259 viral genomes present. Here is the code I used:

time dRep dereplicate drep/ -g /data/ldd/data_for_processing/fna_list.txt -p 128 -l 2000 --S_algorithm fastANI --ignoreGenomeQuality -pa 0.8 -sa 0.97 -nc 0.85 -comW 0 -conW 0 -strW 0 -N50W 0 -sizeW 1 -centW 0 --skip_plots

I checked the logger.log file and I suspect the problem might lie in the second step:dRep dereplicate Step 2. Cluster
The following content is excerpted from logger.log:

09-09 16:09 DEBUG running cluster 221
09-09 16:09 DEBUG /home/user/miniconda3/envs/checkm1/bin/fastANI --ql /data/ldd/data_for_processing/drep/data/fastANI_files/tmp/genomeList --rl /data/ldd/data_for_processing/drep/data/fastANI_files/tmp/genomeList -o /data/ldd/data_for_processing/drep/data/fastANI_files/fastANI_out_xoimckskpn --matrix -t 128 --minFraction 0 xoimckskpn
09-09 16:09 DEBUG running cluster 5566
09-09 16:09 DEBUG /home/user/miniconda3/envs/checkm1/bin/fastANI --ql /data/ldd/data_for_processing/drep/data/fastANI_files/tmp/genomeList --rl /data/ldd/data_for_processing/drep/data/fastANI_files/tmp/genomeList -o /data/ldd/data_for_processing/drep/data/fastANI_files/fastANI_out_imxwmalabg --matrix -t 128 --minFraction 0 imxwmalabg
09-09 16:09 ERROR CRITICAL ERROR WITH SECONDARY CLUSTERING CODE imxwmalabg; SKIPPING
09-09 16:09 ERROR CRITICAL ERROR WITH PRIMARY CLUSTER 5566; TRYING AGAIN
09-09 16:09 DEBUG /home/user/miniconda3/envs/checkm1/bin/fastANI --ql /data/ldd/data_for_processing/drep/data/fastANI_files/tmp/genomeList --rl /data/ldd/data_for_processing/drep/data/fastANI_files/tmp/genomeList -o /data/ldd/data_for_processing/drep/data/fastANI_files/fastANI_out_mhnylcorro --matrix -t 128 --minFraction 0 mhnylcorro
09-09 16:09 ERROR CRITICAL ERROR WITH SECONDARY CLUSTERING CODE mhnylcorro; SKIPPING
09-09 16:09 ERROR DOUBLE CRITICAL ERROR AGAIN WITH PRIMARY CLUSTER 5566; SKIPPING
09-09 16:09 DEBUG running cluster 11328
09-09 16:09 DEBUG /home/user/miniconda3/envs/checkm1/bin/fastANI --ql /data/ldd/data_for_processing/drep/data/fastANI_files/tmp/genomeList --rl /data/ldd/data_for_processing/drep/data/fastANI_files/tmp/genomeList -o /data/ldd/data_for_processing/drep/data/fastANI_files/fastANI_out_fnuwccsket --matrix -t 128 --minFraction 0 fnuwccsket

But I don't know how to solve this problem.

Thank you!

[MrOlm]

Huh- that error means that something is going wrong with the fastANI clustering. You could try a different secondary clustering alogrithm, or you could run in debug mode (-d) and look at the output in the cmd_logs folder in the log output folder to see if fastANI is throwing any errors

Matt

[Hundred56]

Huh- that error means that something is going wrong with the fastANI clustering. You could try a different secondary clustering alogrithm, or you could run in debug mode (-d) and look at the output in the cmd_logs folder in the log output folder to see if fastANI is throwing any errors

Matt

Thank you for your reply!
In fact, when I later resumed using dRep, I chose the default clustering algorithm. But the same error is still displayed.
The following is the content of cmd logs when I use debug mode -d:

Reference = [/data/ldd/test/test_dRep/L1EHI2603397--WuXi_9_A__vRhyme_100.fna]
Query = [/data/ldd/test/test_dRep/L1EHI2603397--WuXi_9_A__vRhyme_100.fna]
Kmer size = 16
Fragment length = 3000
Threads = 128
ANI output file = /data/ldd/data_for_processing/drep_test/data/fastANI_files/fastANI_out_fiaevjanej
Sanity Check = 0

INFO [thread 0], skch::main, Count of threads executing parallel_for : 128
INFO [thread 0], skch::Sketch::build, window size for minimizer sampling = 24
INFO [thread 124], skch::main, ready to exit the loop
INFO [thread 116], skch::main, ready to exit the loop
INFO [thread 43], skch::main, ready to exit the loop
INFO [thread 67], skch::main, ready to exit the loop
INFO [thread 69], skch::main, ready to exit the loop
INFO [thread 125], skch::main, ready to exit the loop
INFO [thread 37], skch::main, ready to exit the loop
INFO [thread 0], skch::Sketch::build, minimizers picked from reference = 1589
INFO [thread 93], skch::main, ready to exit the loop
INFO [thread 15], skch::main, ready to exit the loop
INFO [thread 94], skch::main, ready to exit the loop
INFO [thread 52], skch::main, ready to exit the loop
INFO [thread 109], skch::main, ready to exit the loop
INFO [thread 20], skch::main, ready to exit the loop
INFO [thread 86], skch::main, ready to exit the loop
INFO [thread 0], skch::Sketch::index, unique minimizers = 1578
INFO [thread 0], skch::Sketch::computeFreqHist, Frequency histogram of minimizers = (1, 1568) ... INFO [thread 18(3, 1], skch::main, ready to exit the loop
INFO [thread 19], skch::main, ready to exit the loop)
INFO [thread 0], skch::Sketch::computeFreqHist, consider all minimizers during lookup.
INFO [thread 0], skch::main, Time spent sketching the reference :
INFO [thread 61], skch::main, ready to exit the loop
INFO [thread 45], skch::main, ready to exit the loop
0.00706612 sec
INFO [thread 0], skch::main, Start Map 1
INFO [thread 35], skch::main, ready to exit the loop
INFO [thread 16], skch::main, ready to exit the loop
INFO [thread 117], skch::main, ready to exit the loop
INFO [thread 77], skch::main, ready to exit the loop
INFO [thread 46], skch::main, ready to exit the loop
INFO [thread 28], skch::main, ready to exit the loop
INFO [thread 119], skch::main, ready to exit the loop
INFO [thread 89], skch::main, ready to exit the loop
INFO [thread 75], skch::main, ready to exit the loop
INFO [thread 84], skch::main, ready to exit the loop
INFO [thread 51], skch::main, ready to exit the loop
INFO [thread 30], skch::main, ready to exit the loop
INFO [thread 0], skch::main, Time spent mapping fragments in query #1 : 0.00156651 sec
INFO [thread 0], skch::main, Time spent post mapping : 1.7e-06 sec
INFO [thread 0], skch::main, ready to exit the loop
INFO [thread 27], skch::main, ready to exit the loop
INFO [thread 59], skch::main, ready to exit the loop
INFO [thread 81], skch::main, ready to exit the loop
INFO [thread 12], skch::main, ready to exit the loop
INFO [thread 60], skch::main, ready to exit the loop
INFO [thread 11], skch::main, ready to exit the loop
INFO [thread 25], skch::main, ready to exit the loop
INFO [thread 23], skch::main, ready to exit the loop
INFO [thread 13], skch::main, ready to exit the loop
INFO [thread 122], skch::main, ready to exit the loop
INFO [thread 126], skch::main, ready to exit the loop
INFO [thread 91], skch::main, ready to exit the loop
INFO [thread 107], skch::main, ready to exit the loop
INFO [thread 10], skch::main, ready to exit the loop
INFO [thread 36], skch::main, ready to exit the loop
INFO [thread 96], skch::main, ready to exit the loop
INFO [thread 54], skch::main, ready to exit the loop
INFO [thread 102], skch::main, ready to exit the loop
INFO [thread 58], skch::main, ready to exit the loop
INFO [thread 29], skch::main, ready to exit the loop
INFO [thread 101], skch::main, ready to exit the loop
INFO [thread 104], skch::main, ready to exit the loop
INFO [thread 49], skch::main, ready to exit the loop
INFO [thread 33], skch::main, ready to exit the loop
INFO [thread 98], skch::main, ready to exit the loop
INFO [thread 85], skch::main, ready to exit the loop
INFO [thread 105], skch::main, ready to exit the loop
INFO [thread 100], skch::main, ready to exit the loop
INFO [thread 87], skch::main, ready to exit the loop
INFO [thread 115], skch::main, ready to exit the loop
INFO [thread 57], skch::main, ready to exit the loop
INFO [thread 6], skch::main, ready to exit the loop
INFO [thread 44], skch::main, ready to exit the loop
INFO [thread 55], skch::main, ready to exit the loop
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INFO [thread 95], skch::main, ready to exit the loop
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INFO [thread 38], skch::main, ready to exit the loop
INFO [thread 106], skch::main, ready to exit the loop
INFO [thread 110], skch::main, ready to exit the loop
INFO [thread 76], skch::main, ready to exit the loop
INFO [thread 70], skch::main, ready to exit the loop
INFO [thread 63], skch::main, ready to exit the loop
INFO [thread 31], skch::main, ready to exit the loop
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INFO [thread 90], skch::main, ready to exit the loop
INFO [thread 21], skch::main, ready to exit the loop
INFO [thread 97], skch::main, ready to exit the loop
INFO [thread 80], skch::main, ready to exit the loop
INFO [thread 88], skch::main, ready to exit the loop
INFO [thread 8], skch::main, ready to exit the loop
INFO [thread 14], skch::main, ready to exit the loop
INFO [thread 74], skch::main, ready to exit the loop
INFO [thread 103], skch::main, ready to exit the loop
INFO [thread 40], skch::main, ready to exit the loop
INFO [thread 17], skch::main, ready to exit the loop
INFO [thread 68], skch::main, ready to exit the loop
INFO [thread 1], skch::main, ready to exit the loop
INFO [thread 127], skch::main, ready to exit the loop
INFO [thread 26], skch::main, ready to exit the loop
INFO [thread 120], skch::main, ready to exit the loop
INFO [thread 47], skch::main, ready to exit the loop
INFO [thread 111], skch::main, ready to exit the loop
INFO [thread 92], skch::main, ready to exit the loop
INFO [thread 2], skch::main, ready to exit the loop
INFO [thread 82], skch::main, ready to exit the loop
INFO [thread 99], skch::main, ready to exit the loop
INFO [thread 65], skch::main, ready to exit the loop
INFO [thread 78], skch::main, ready to exit the loop
INFO [thread 62], skch::main, ready to exit the loop
INFO [thread 42], skch::main, ready to exit the loop
INFO [thread 72], skch::main, ready to exit the loop
INFO [thread 48], skch::main, ready to exit the loop
INFO [thread 7], skch::main, ready to exit the loop
INFO [thread 108], skch::main, ready to exit the loop
INFO [thread 3], skch::main, ready to exit the loop
INFO [thread 53], skch::main, ready to exit the loop
INFO [thread 121], skch::main, ready to exit the loop
INFO [thread 118], skch::main, ready to exit the loop
INFO [thread 112], skch::main, ready to exit the loop
INFO [thread 64], skch::main, ready to exit the loop
INFO [thread 113], skch::main, ready to exit the loop
INFO [thread 123], skch::main, ready to exit the loop
INFO [thread 56], skch::main, ready to exit the loop
INFO [thread 71], skch::main, ready to exit the loop
INFO [thread 24], skch::main, ready to exit the loop
INFO [thread 41], skch::main, ready to exit the loop
INFO [thread 50], skch::main, ready to exit the loop
INFO [thread 83], skch::main, ready to exit the loop
INFO [thread 4], skch::main, ready to exit the loop
INFO [thread 32], skch::main, ready to exit the loop
INFO [thread 5], skch::main, ready to exit the loop
INFO [thread 114], skch::main, ready to exit the loop
INFO [thread 22], skch::main, ready to exit the loop
INFO [thread 73], skch::main, ready to exit the loop
INFO, skch::main, parallel_for execution finished

[Cczyf]

Huh- that error means that something is going wrong with the fastANI clustering. You could try a different secondary clustering alogrithm, or you could run in debug mode (-d) and look at the output in the cmd_logs folder in the log output folder to see if fastANI is throwing any errors这个错误意味着fastANI集群出了问题。您可以尝试不同的辅助集群算法，或者您可以在调试模式下运行（），并查看输出文件夹中的文件夹中的输出，以查看fastANI是否抛出任何错误
Matt 马特

Thank you for your reply!谢谢您的回复！ In fact, when I later resumed using dRep, I chose the default clustering algorithm. But the same error is still displayed.事实上，当我后来恢复使用dRep时，我选择了默认的聚类算法。但是仍然显示相同的错误。 The following is the content of cmd logs when I use debug mode -d:以下是使用调试模式-d时的cmd日志内容：

Reference = [/data/ldd/test/test_dRep/L1EHI2603397--WuXi_9_A__vRhyme_100.fna]参考文献= [/data/ldd/test/test_dRep/L1EHI2603397—WuXi_9_A__vRhyme_100.fna] Query = [/data/ldd/test/test_dRep/L1EHI2603397--WuXi_9_A__vRhyme_100.fna]Query = [/data/ldd/test/test_dRep/L1EHI2603397—WuXi_9_A__vRhyme_100.fna] Kmer size = 16 Kmer尺寸= 16 Fragment length = 3000 片段长度= 3000 Threads = 128 线程数= 128 ANI output file = /data/ldd/data_for_processing/drep_test/data/fastANI_files/fastANI_out_fiaevjanejANI输出文件= /data/ldd/data_for_processing/drep_test/data/fastANI_files/fastANI_out_fiaevjanej Sanity Check = 0完整性检查= 0

INFO [thread 0], skch::main, Count of threads executing parallel_for : 128INFO [thread 0], skch::main，执行parallel_for的线程数：128 INFO [thread 0], skch::Sketch::build, window size for minimizer sampling = 24INFO[线程0]，skch::Sketch::build，最小化采样的窗口大小= 24 INFO [thread 124], skch::main, ready to exit the loopINFO[线程124]，skch::main，准备退出循环 INFO [thread 116], skch::main, ready to exit the loopINFO[线程116]，skch::main，准备退出循环 INFO [thread 43], skch::main, ready to exit the loopINFO[线程43]，skch::main，准备退出循环 INFO [thread 67], skch::main, ready to exit the loopINFO[线程67]，skch::main，准备退出循环 INFO [thread 69], skch::main, ready to exit the loopINFO[线程69]，skch::main，准备退出循环 INFO [thread 125], skch::main, ready to exit the loopINFO[线程125]，skch::main，准备退出循环 INFO [thread 37], skch::main, ready to exit the loopINFO[线程37]，skch::main，准备退出循环 INFO [thread 0], skch::Sketch::build, minimizers picked from reference = 1589INFO [thread 0], skch::Sketch::build, minimizers from reference = 1589 INFO [thread 93], skch::main, ready to exit the loopINFO[线程93]，skch::main，准备退出循环 INFO [thread 15], skch::main, ready to exit the loopINFO[线程15]，skch::main，准备退出循环 INFO [thread 94], skch::main, ready to exit the loopINFO[线程94]，skch::main，准备退出循环 INFO [thread 52], skch::main, ready to exit the loopINFO[线程52]，skch::main，准备退出循环 INFO [thread 109], skch::main, ready to exit the loopINFO[线程109]，skch::main，准备退出循环 INFO [thread 20], skch::main, ready to exit the loopINFO[线程20]，skch::main，准备退出循环 INFO [thread 86], skch::main, ready to exit the loopINFO[线程86]，skch::main，准备退出循环 INFO [thread 0], skch::Sketch::index, unique minimizers = 1578INFO[线程0]，skch::Sketch::index，唯一最小值= 1578 INFO [thread 0], skch::Sketch::computeFreqHist, Frequency histogram of minimizers = (1, 1568) ... INFO [thread 18(3, 1], skch::main, ready to exit the loopINFO [thread 0], skch::Sketch::computeFreqHist，频率直方图=(1,1568)…INFO [thread 18(3,1)], skch::main，准备退出循环 INFO [thread 19], skch::main, ready to exit the loop)INFO[线程19]，skch::main，准备退出循环) INFO [thread 0], skch::Sketch::computeFreqHist, consider all minimizers during lookup.INFO [thread 0], skch::Sketch::computeFreqHist，查找时考虑所有的最小化。 INFO [thread 0], skch::main, Time spent sketching the reference :INFO [thread 0], skch::main，绘制引用的时间 INFO [thread 61], skch::main, ready to exit the loopINFO[线程61]，skch::main，准备退出循环 INFO [thread 45], skch::main, ready to exit the loopINFO[线程45]，skch::main，准备退出循环 0.00706612 sec 0.00706612秒 INFO [thread 0], skch::main, Start Map 1INFO[线程0]，skch::main，开始映射1 INFO [thread 35], skch::main, ready to exit the loopINFO [thread 35], skch::main，准备退出循环 INFO [thread 16], skch::main, ready to exit the loopINFO[线程16]，skch::main，准备退出循环 INFO [thread 117], skch::main, ready to exit the loopINFO[线程117]，skch::main，准备退出循环 INFO [thread 77], skch::main, ready to exit the loopINFO[线程77]，skch::main，准备退出循环 INFO [thread 46], skch::main, ready to exit the loopINFO[线程46]，skch::main，准备退出循环 INFO [thread 28], skch::main, ready to exit the loopINFO[线程28]，skch::main，准备退出循环 INFO [thread 119], skch::main, ready to exit the loopINFO[线程119]，skch::main，准备退出循环 INFO [thread 89], skch::main, ready to exit the loopINFO[线程89]，skch::main，准备退出循环 INFO [thread 75], skch::main, ready to exit the loopINFO[线程75]，skch::main，准备退出循环 INFO [thread 84], skch::main, ready to exit the loopINFO[线程84]，skch::main，准备退出循环 INFO [thread 51], skch::main, ready to exit the loop INFO [thread 30], skch::main, ready to exit the loop INFO [thread 0], skch::main, Time spent mapping fragments in query #1 : 0.00156651 sec INFO [thread 0], skch::main, Time spent post mapping : 1.7e-06 sec INFO [thread 0], skch::main, ready to exit the loop INFO [thread 27], skch::main, ready to exit the loop INFO [thread 59], skch::main, ready to exit the loop INFO [thread 81], skch::main, ready to exit the loop INFO [thread 12], skch::main, ready to exit the loop INFO [thread 60], skch::main, ready to exit the loop INFO [thread 11], skch::main, ready to exit the loop INFO [thread 25], skch::main, ready to exit the loop INFO [thread 23], skch::main, ready to exit the loop INFO [thread 13], skch::main, ready to exit the loop INFO [thread 122], skch::main, ready to exit the loop INFO [thread 126], skch::main, ready to exit the loop INFO [thread 91], skch::main, ready to exit the loop INFO [thread 107], skch::main, ready to exit the loop INFO [thread 10], skch::main, ready to exit the loop INFO [thread 36], skch::main, ready to exit the loop INFO [thread 96], skch::main, ready to exit the loop INFO [thread 54], skch::main, ready to exit the loop INFO [thread 102], skch::main, ready to exit the loop INFO [thread 58], skch::main, ready to exit the loop INFO [thread 29], skch::main, ready to exit the loop INFO [thread 101], skch::main, ready to exit the loop INFO [thread 104], skch::main, ready to exit the loop INFO [thread 49], skch::main, ready to exit the loop INFO [thread 33], skch::main, ready to exit the loop INFO [thread 98], skch::main, ready to exit the loop INFO [thread 85], skch::main, ready to exit the loop INFO [thread 105], skch::main, ready to exit the loop INFO [thread 100], skch::main, ready to exit the loop INFO [thread 87], skch::main, ready to exit the loop INFO [thread 115], skch::main, ready to exit the loop INFO [thread 57], skch::main, ready to exit the loop INFO [thread 6], skch::main, ready to exit the loop INFO [thread 44], skch::main, ready to exit the loop INFO [thread 55], skch::main, ready to exit the loop INFO [thread 39], skch::main, ready to exit the loop INFO [thread 66], skch::main, ready to exit the loop INFO [thread 95], skch::main, ready to exit the loop INFO [thread 9], skch::main, ready to exit the loop INFO [thread 38], skch::main, ready to exit the loop INFO [thread 106], skch::main, ready to exit the loop INFO [thread 110], skch::main, ready to exit the loop INFO [thread 76], skch::main, ready to exit the loop INFO [thread 70], skch::main, ready to exit the loop INFO [thread 63], skch::main, ready to exit the loop INFO [thread 31], skch::main, ready to exit the loop INFO [thread 79], skch::main, ready to exit the loop INFO [thread 34], skch::main, ready to exit the loop INFO [thread 90], skch::main, ready to exit the loop INFO [thread 21], skch::main, ready to exit the loop INFO [thread 97], skch::main, ready to exit the loop INFO [thread 80], skch::main, ready to exit the loop INFO [thread 88], skch::main, ready to exit the loop INFO [thread 8], skch::main, ready to exit the loop INFO [thread 14], skch::main, ready to exit the loop INFO [thread 74], skch::main, ready to exit the loop INFO [thread 103], skch::main, ready to exit the loop INFO [thread 40], skch::main, ready to exit the loop INFO [thread 17], skch::main, ready to exit the loop INFO [thread 68], skch::main, ready to exit the loop INFO [thread 1], skch::main, ready to exit the loop INFO [thread 127], skch::main, ready to exit the loop INFO [thread 26], skch::main, ready to exit the loop INFO [thread 120], skch::main, ready to exit the loop INFO [thread 47], skch::main, ready to exit the loop INFO [thread 111], skch::main, ready to exit the loop INFO [thread 92], skch::main, ready to exit the loop INFO [thread 2], skch::main, ready to exit the loop INFO [thread 82], skch::main, ready to exit the loop INFO [thread 99], skch::main, ready to exit the loop INFO [thread 65], skch::main, ready to exit the loop INFO [thread 78], skch::main, ready to exit the loop INFO [thread 62], skch::main, ready to exit the loop INFO [thread 42], skch::main, ready to exit the loop INFO [thread 72], skch::main, ready to exit the loop INFO [thread 48], skch::main, ready to exit the loop INFO [thread 7], skch::main, ready to exit the loop INFO [thread 108], skch::main, ready to exit the loop INFO [thread 3], skch::main, ready to exit the loop INFO [thread 53], skch::main, ready to exit the loop INFO [thread 121], skch::main, ready to exit the loop INFO [thread 118], skch::main, ready to exit the loop INFO [thread 112], skch::main, ready to exit the loop INFO [thread 64], skch::main, ready to exit the loop INFO [thread 113], skch::main, ready to exit the loop INFO [thread 123], skch::main, ready to exit the loop INFO [thread 56], skch::main, ready to exit the loop INFO [thread 71], skch::main, ready to exit the loop INFO [thread 24], skch::main, ready to exit the loop INFO [thread 41], skch::main, ready to exit the loop INFO [thread 50], skch::main, ready to exit the loop INFO [thread 83], skch::main, ready to exit the loop INFO [thread 4], skch::main, ready to exit the loop INFO [thread 32], skch::main, ready to exit the loop INFO [thread 5], skch::main, ready to exit the loop INFO [thread 114], skch::main, ready to exit the loop INFO [thread 22], skch::main, ready to exit the loop INFO [thread 73], skch::main, ready to exit the loop INFO, skch::main, parallel_for execution finished

sorry, have you sloved this problem? I have same errors

[maggieweng]

Hi, I just want to flag that I am getting the same error message when running dRep. I ran checkM externally and passed my genomeInfo file to dRep; 116 genomes passed initial quality filtering. Primary clusters via MASH were seemingly successful but fastANI fails for secondary clustering. Here is the command I ran (excluding -g since the Bdb is already created): dRep dereplicate /scratch/users/wengm/AT36_MMV19_metagenomes/bin_analysis/drep/ -sa 0.95 -comp 50 -con 10 --S_algorithm fastANI --debug --genomeInfo /scratch/users/wengm/AT36_MMV19_metagenomes/bin_analysis/checkM2/genome_information.csv. Here is an excerpt of logger.log:

`***************************************************
..:: dRep dereplicate Step 1. Filter ::..

---

Will filter Bdb
116 genomes were input to dRep
Calculating genome info of genomes
100.00% of genomes passed length filtering
100.00% of genomes passed checkM filtering

---

..:: dRep dereplicate Step 2. Cluster ::..

---

Running primary clustering
Nevermind! Loading cached primary clustering
2. Primary clustering cache loaded
64 primary clusters made
Running secondary clustering
Running 330 fastANI comparisons- should take ~ 28.3 min
CRITICAL ERROR WITH SECONDARY CLUSTERING CODE leolkbmpeq; SKIPPING
CRITICAL ERROR WITH PRIMARY CLUSTER 33; TRYING AGAIN
CRITICAL ERROR WITH SECONDARY CLUSTERING CODE ocqudphgvs; SKIPPING
DOUBLE CRITICAL ERROR AGAIN WITH PRIMARY CLUSTER 33; SKIPPING
CRITICAL ERROR WITH SECONDARY CLUSTERING CODE jrvrmnddpk; SKIPPING
CRITICAL ERROR WITH PRIMARY CLUSTER 28; TRYING AGAIN
CRITICAL ERROR WITH SECONDARY CLUSTERING CODE zmlxbagzrr; SKIPPING
DOUBLE CRITICAL ERROR AGAIN WITH PRIMARY CLUSTER 28; SKIPPING`

etc...ending with the following error message:
Traceback (most recent call last):
File "/share/software/user/open/py-drep/3.4.2_py312/bin/dRep", line 32, in
Controller().parseArguments(args)
File "/share/software/user/open/py-drep/3.4.2_py312/lib/python3.12/site-packages/drep/controller.py", line 100, in parseArguments
self.dereplicate_operation(**vars(args))
File "/share/software/user/open/py-drep/3.4.2_py312/lib/python3.12/site-packages/drep/controller.py", line 48, in dereplicate_operation
drep.d_workflows.dereplicate_wrapper(kwargs['work_directory'],**kwargs)
File "/share/software/user/open/py-drep/3.4.2_py312/lib/python3.12/site-packages/drep/d_workflows.py", line 37, in dereplicate_wrapper
drep.d_cluster.controller.d_cluster_wrapper(wd, **kwargs)
File "/share/software/user/open/py-drep/3.4.2_py312/lib/python3.12/site-packages/drep/d_cluster/controller.py", line 179, in d_cluster_wrapper
GenomeClusterController(workDirectory, **kwargs).main()
File "/share/software/user/open/py-drep/3.4.2_py312/lib/python3.12/site-packages/drep/d_cluster/controller.py", line 35, in main
self.run_secondary_clustering()
File "/share/software/user/open/py-drep/3.4.2_py312/lib/python3.12/site-packages/drep/d_cluster/controller.py", line 140, in run_secondary_clustering
Ndb, Cdb, c2ret = drep.d_cluster.compare_utils.secondary_clustering(self.Bdb, self.MCdb, algorithm, self.wd.get_dir('data'), wd=self.wd, **self.kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/share/software/user/open/py-drep/3.4.2_py312/lib/python3.12/site-packages/drep/d_cluster/compare_utils.py", line 311, in secondary_clustering
Cdb, c2ret = drep.d_cluster.utils._cluster_Ndb(Ndb, comp_method=algorithm, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/share/software/user/open/py-drep/3.4.2_py312/lib/python3.12/site-packages/drep/d_cluster/utils.py", line 49, in _cluster_Ndb
for name, ndb in Ndb.groupby(id):
^^^^^^^^^^^^^^^
File "/share/software/user/open/py-pandas/2.2.1_py312/lib/python3.12/site-packages/pandas/core/frame.py", line 9170, in groupby
return DataFrameGroupBy(
^^^^^^^^^^^^^^^^^
File "/share/software/user/open/py-pandas/2.2.1_py312/lib/python3.12/site-packages/pandas/core/groupby/groupby.py", line 1329, in init
grouper, exclusions, obj = get_grouper(
^^^^^^^^^^^^
File "/share/software/user/open/py-pandas/2.2.1_py312/lib/python3.12/site-packages/pandas/core/groupby/grouper.py", line 1043, in get_grouper
raise KeyError(gpr)
KeyError: 'primary_cluster'

The cmd.log reports the following:

Reference = [/scratch/users/wengm/AT36_MMV19_metagenomes/metabat/bins/SW_PC7_36.4.fa, /scratch/users/wengm/AT36_MMV19_metagenomes/metabat/bins/SW_PC7_69.19.fa]
Query = [/scratch/users/wengm/AT36_MMV19_metagenomes/metabat/bins/SW_PC7_36.4.fa, /scratch/users/wengm/AT36_MMV19_metagenomes/metabat/bins/SW_PC7_69.19.fa]
Kmer size = 16
Fragment length = 3000
Threads = 6
ANI output file = /scratch/users/wengm/AT36_MMV19_metagenomes/bin_analysis/drep/data/fastANI_files/fastANI_out_mmkkyxpkyu
Sanity Check = 0

INFO [thread 0], skch::main, Count of threads executing parallel_for : 6
INFO [thread 0], skch::Sketch::build, window size for minimizer sampling = 24
INFO [thread 0], skch::Sketch::build, minimizers picked from reference = 49385
INFO [thread 4], skch::main, ready to exit the loop
INFO [thread 5], skch::main, ready to exit the loop
INFO [thread 3], skch::main, ready to exit the loop
INFO [thread 2], skch::main, ready to exit the loop
INFO [thread 0], skch::Sketch::index, unique minimizers = 49099
INFO [thread 0], skch::Sketch::computeFreqHist, Frequency histogram of minimizers = (1, 48892) ... (7, 3)
INFO [thread 0], skch::Sketch::computeFreqHist, consider all minimizers during lookup.
INFO [thread 0], skch::main, Time spent sketching the reference : 0.209903 sec
INFO [thread 0], skch::main, Start Map 1
INFO [thread 0], skch::main, Time spent mapping fragments in query #1 : 0.0482654 sec
INFO [thread 0], skch::main, Time spent post mapping : 1.5428e-05 sec
INFO [thread 0], skch::main, Start Map 2
INFO [thread 0], skch::main, Time spent mapping fragments in query #2 : 0.0565293 sec
INFO [thread 0], skch::main, Time spent post mapping : 1.2263e-05 sec
INFO [thread 0], skch::main, ready to exit the loop
INFO [thread 1], skch::main, ready to exit the loop
INFO, skch::main, parallel_for execution finished

I can't figure out the error that fastANI is throwing so I'm pretty stumped.