Job ID = 6367277 SRX = SRX330987 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:28:21 prefetch.2.10.7: 1) Downloading 'SRR947192'... 2020-06-15T23:28:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:33:10 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:33:10 prefetch.2.10.7: 1) 'SRR947192' was downloaded successfully Read 19590984 spots for SRR947192/SRR947192.sra Written 19590984 spots for SRR947192/SRR947192.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:22 19590984 reads; of these: 19590984 (100.00%) were unpaired; of these: 933600 (4.77%) aligned 0 times 12582653 (64.23%) aligned exactly 1 time 6074731 (31.01%) aligned >1 times 95.23% overall alignment rate Time searching: 00:05:22 Overall time: 00:05:22 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4947966 / 18657384 = 0.2652 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:44:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:44:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:44:36: 1000000 INFO @ Tue, 16 Jun 2020 08:44:44: 2000000 INFO @ Tue, 16 Jun 2020 08:44:51: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:44:59: 4000000 INFO @ Tue, 16 Jun 2020 08:44:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:44:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:44:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:45:07: 5000000 INFO @ Tue, 16 Jun 2020 08:45:07: 1000000 INFO @ Tue, 16 Jun 2020 08:45:15: 6000000 INFO @ Tue, 16 Jun 2020 08:45:15: 2000000 INFO @ Tue, 16 Jun 2020 08:45:23: 7000000 INFO @ Tue, 16 Jun 2020 08:45:24: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 08:45:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 16 Jun 2020 08:45:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:45:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:45:31: 8000000 INFO @ Tue, 16 Jun 2020 08:45:32: 4000000 INFO @ Tue, 16 Jun 2020 08:45:37: 1000000 INFO @ Tue, 16 Jun 2020 08:45:39: 9000000 INFO @ Tue, 16 Jun 2020 08:45:40: 5000000 INFO @ Tue, 16 Jun 2020 08:45:45: 2000000 INFO @ Tue, 16 Jun 2020 08:45:47: 10000000 INFO @ Tue, 16 Jun 2020 08:45:49: 6000000 INFO @ Tue, 16 Jun 2020 08:45:54: 3000000 INFO @ Tue, 16 Jun 2020 08:45:56: 11000000 INFO @ Tue, 16 Jun 2020 08:45:57: 7000000 INFO @ Tue, 16 Jun 2020 08:46:02: 4000000 INFO @ Tue, 16 Jun 2020 08:46:04: 12000000 INFO @ Tue, 16 Jun 2020 08:46:05: 8000000 INFO @ Tue, 16 Jun 2020 08:46:10: 5000000 INFO @ Tue, 16 Jun 2020 08:46:13: 13000000 INFO @ Tue, 16 Jun 2020 08:46:14: 9000000 INFO @ Tue, 16 Jun 2020 08:46:18: 6000000 INFO @ Tue, 16 Jun 2020 08:46:19: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:46:19: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:46:19: #1 total tags in treatment: 13709418 INFO @ Tue, 16 Jun 2020 08:46:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:46:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:46:19: #1 tags after filtering in treatment: 13709418 INFO @ Tue, 16 Jun 2020 08:46:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:46:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:46:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:46:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:46:20: #2 number of paired peaks: 908 WARNING @ Tue, 16 Jun 2020 08:46:20: Fewer paired peaks (908) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 908 pairs to build model! INFO @ Tue, 16 Jun 2020 08:46:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:46:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:46:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:46:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:46:20: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:46:20: #2 alternative fragment length(s) may be 1,16,18,35,573,590 bps INFO @ Tue, 16 Jun 2020 08:46:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.05_model.r WARNING @ Tue, 16 Jun 2020 08:46:20: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:46:20: #2 You may need to consider one of the other alternative d(s): 1,16,18,35,573,590 WARNING @ Tue, 16 Jun 2020 08:46:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:46:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:46:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:46:22: 10000000 INFO @ Tue, 16 Jun 2020 08:46:26: 7000000 INFO @ Tue, 16 Jun 2020 08:46:31: 11000000 INFO @ Tue, 16 Jun 2020 08:46:34: 8000000 INFO @ Tue, 16 Jun 2020 08:46:39: 12000000 INFO @ Tue, 16 Jun 2020 08:46:42: 9000000 INFO @ Tue, 16 Jun 2020 08:46:44: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:46:47: 13000000 INFO @ Tue, 16 Jun 2020 08:46:50: 10000000 INFO @ Tue, 16 Jun 2020 08:46:53: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:46:53: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:46:53: #1 total tags in treatment: 13709418 INFO @ Tue, 16 Jun 2020 08:46:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:46:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:46:53: #1 tags after filtering in treatment: 13709418 INFO @ Tue, 16 Jun 2020 08:46:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:46:53: #1 finished! INFO @ Tue, 16 Jun 2020 08:46:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:46:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:46:54: #2 number of paired peaks: 908 WARNING @ Tue, 16 Jun 2020 08:46:54: Fewer paired peaks (908) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 908 pairs to build model! INFO @ Tue, 16 Jun 2020 08:46:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:46:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:46:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:46:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:46:54: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:46:54: #2 alternative fragment length(s) may be 1,16,18,35,573,590 bps INFO @ Tue, 16 Jun 2020 08:46:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.10_model.r WARNING @ Tue, 16 Jun 2020 08:46:54: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:46:54: #2 You may need to consider one of the other alternative d(s): 1,16,18,35,573,590 WARNING @ Tue, 16 Jun 2020 08:46:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:46:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:46:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:46:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:46:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:46:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.05_summits.bed INFO @ Tue, 16 Jun 2020 08:46:56: Done! pass1 - making usageList (0 chroms): 3 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:46:58: 11000000 INFO @ Tue, 16 Jun 2020 08:47:05: 12000000 INFO @ Tue, 16 Jun 2020 08:47:13: 13000000 INFO @ Tue, 16 Jun 2020 08:47:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:47:18: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:47:18: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:47:18: #1 total tags in treatment: 13709418 INFO @ Tue, 16 Jun 2020 08:47:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:47:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:47:18: #1 tags after filtering in treatment: 13709418 INFO @ Tue, 16 Jun 2020 08:47:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:47:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:47:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:47:18: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:47:19: #2 number of paired peaks: 908 WARNING @ Tue, 16 Jun 2020 08:47:19: Fewer paired peaks (908) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 908 pairs to build model! INFO @ Tue, 16 Jun 2020 08:47:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:47:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:47:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:47:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:47:19: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:47:19: #2 alternative fragment length(s) may be 1,16,18,35,573,590 bps INFO @ Tue, 16 Jun 2020 08:47:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.20_model.r WARNING @ Tue, 16 Jun 2020 08:47:19: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:47:19: #2 You may need to consider one of the other alternative d(s): 1,16,18,35,573,590 WARNING @ Tue, 16 Jun 2020 08:47:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 08:47:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:47:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:47:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:47:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:47:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.10_summits.bed INFO @ Tue, 16 Jun 2020 08:47:29: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:47:43: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:47:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:47:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:47:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX330987/SRX330987.20_summits.bed INFO @ Tue, 16 Jun 2020 08:47:55: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling