Job ID = 6527402 SRX = SRX172526 Genome = ce10 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:17:38 prefetch.2.10.7: 1) Downloading 'SRR530781'... 2020-06-29T12:17:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:23:04 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:23:04 prefetch.2.10.7: 1) 'SRR530781' was downloaded successfully Read 32252152 spots for SRR530781/SRR530781.sra Written 32252152 spots for SRR530781/SRR530781.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: 00:07:49 32252152 reads; of these: 32252152 (100.00%) were unpaired; of these: 2876810 (8.92%) aligned 0 times 23295662 (72.23%) aligned exactly 1 time 6079680 (18.85%) aligned >1 times 91.08% overall alignment rate Time searching: 00:07:49 Overall time: 00:07:49 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 12 files... [bam_rmdupse_core] 6187411 / 29375342 = 0.2106 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 @ Mon, 29 Jun 2020 21:46:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.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 @ Mon, 29 Jun 2020 21:46:29: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:46:29: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:46:34: 1000000 INFO @ Mon, 29 Jun 2020 21:46:40: 2000000 INFO @ Mon, 29 Jun 2020 21:46:45: 3000000 INFO @ Mon, 29 Jun 2020 21:46:51: 4000000 INFO @ Mon, 29 Jun 2020 21:46:56: 5000000 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 @ Mon, 29 Jun 2020 21:46:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.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 @ Mon, 29 Jun 2020 21:46:58: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:46:58: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:47:01: 6000000 INFO @ Mon, 29 Jun 2020 21:47:04: 1000000 INFO @ Mon, 29 Jun 2020 21:47:07: 7000000 INFO @ Mon, 29 Jun 2020 21:47:09: 2000000 INFO @ Mon, 29 Jun 2020 21:47:12: 8000000 INFO @ Mon, 29 Jun 2020 21:47:15: 3000000 INFO @ Mon, 29 Jun 2020 21:47:18: 9000000 INFO @ Mon, 29 Jun 2020 21:47:20: 4000000 INFO @ Mon, 29 Jun 2020 21:47:23: 10000000 INFO @ Mon, 29 Jun 2020 21:47:25: 5000000 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 @ Mon, 29 Jun 2020 21:47:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.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 @ Mon, 29 Jun 2020 21:47:29: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:47:29: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:47:29: 11000000 INFO @ Mon, 29 Jun 2020 21:47:31: 6000000 INFO @ Mon, 29 Jun 2020 21:47:33: 1000000 INFO @ Mon, 29 Jun 2020 21:47:34: 12000000 INFO @ Mon, 29 Jun 2020 21:47:36: 7000000 INFO @ Mon, 29 Jun 2020 21:47:38: 2000000 INFO @ Mon, 29 Jun 2020 21:47:40: 13000000 INFO @ Mon, 29 Jun 2020 21:47:42: 8000000 INFO @ Mon, 29 Jun 2020 21:47:43: 3000000 INFO @ Mon, 29 Jun 2020 21:47:45: 14000000 INFO @ Mon, 29 Jun 2020 21:47:47: 9000000 INFO @ Mon, 29 Jun 2020 21:47:48: 4000000 INFO @ Mon, 29 Jun 2020 21:47:51: 15000000 INFO @ Mon, 29 Jun 2020 21:47:52: 10000000 INFO @ Mon, 29 Jun 2020 21:47:53: 5000000 INFO @ Mon, 29 Jun 2020 21:47:56: 16000000 INFO @ Mon, 29 Jun 2020 21:47:57: 6000000 INFO @ Mon, 29 Jun 2020 21:47:57: 11000000 INFO @ Mon, 29 Jun 2020 21:48:01: 17000000 INFO @ Mon, 29 Jun 2020 21:48:02: 7000000 INFO @ Mon, 29 Jun 2020 21:48:03: 12000000 INFO @ Mon, 29 Jun 2020 21:48:07: 18000000 INFO @ Mon, 29 Jun 2020 21:48:07: 8000000 INFO @ Mon, 29 Jun 2020 21:48:08: 13000000 INFO @ Mon, 29 Jun 2020 21:48:11: 19000000 INFO @ Mon, 29 Jun 2020 21:48:12: 9000000 INFO @ Mon, 29 Jun 2020 21:48:13: 14000000 INFO @ Mon, 29 Jun 2020 21:48:16: 10000000 INFO @ Mon, 29 Jun 2020 21:48:17: 20000000 INFO @ Mon, 29 Jun 2020 21:48:19: 15000000 INFO @ Mon, 29 Jun 2020 21:48:21: 11000000 INFO @ Mon, 29 Jun 2020 21:48:22: 21000000 INFO @ Mon, 29 Jun 2020 21:48:24: 16000000 INFO @ Mon, 29 Jun 2020 21:48:26: 12000000 INFO @ Mon, 29 Jun 2020 21:48:27: 22000000 INFO @ Mon, 29 Jun 2020 21:48:29: 17000000 INFO @ Mon, 29 Jun 2020 21:48:30: 13000000 INFO @ Mon, 29 Jun 2020 21:48:33: 23000000 INFO @ Mon, 29 Jun 2020 21:48:34: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 21:48:34: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 21:48:34: #1 total tags in treatment: 23187931 INFO @ Mon, 29 Jun 2020 21:48:34: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:48:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:48:34: #1 tags after filtering in treatment: 23187931 INFO @ Mon, 29 Jun 2020 21:48:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:48:34: #1 finished! INFO @ Mon, 29 Jun 2020 21:48:34: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:48:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:48:35: 18000000 INFO @ Mon, 29 Jun 2020 21:48:35: 14000000 INFO @ Mon, 29 Jun 2020 21:48:36: #2 number of paired peaks: 219 WARNING @ Mon, 29 Jun 2020 21:48:36: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Mon, 29 Jun 2020 21:48:36: start model_add_line... INFO @ Mon, 29 Jun 2020 21:48:36: start X-correlation... INFO @ Mon, 29 Jun 2020 21:48:36: end of X-cor INFO @ Mon, 29 Jun 2020 21:48:36: #2 finished! INFO @ Mon, 29 Jun 2020 21:48:36: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 21:48:36: #2 alternative fragment length(s) may be 1,22,44,541 bps INFO @ Mon, 29 Jun 2020 21:48:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.05_model.r WARNING @ Mon, 29 Jun 2020 21:48:36: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:48:36: #2 You may need to consider one of the other alternative d(s): 1,22,44,541 WARNING @ Mon, 29 Jun 2020 21:48:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:48:36: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:48:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:48:39: 19000000 INFO @ Mon, 29 Jun 2020 21:48:40: 15000000 INFO @ Mon, 29 Jun 2020 21:48:44: 20000000 INFO @ Mon, 29 Jun 2020 21:48:45: 16000000 INFO @ Mon, 29 Jun 2020 21:48:50: 21000000 INFO @ Mon, 29 Jun 2020 21:48:50: 17000000 INFO @ Mon, 29 Jun 2020 21:48:55: 18000000 INFO @ Mon, 29 Jun 2020 21:48:55: 22000000 INFO @ Mon, 29 Jun 2020 21:49:00: 23000000 INFO @ Mon, 29 Jun 2020 21:49:00: 19000000 INFO @ Mon, 29 Jun 2020 21:49:01: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 21:49:01: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 21:49:01: #1 total tags in treatment: 23187931 INFO @ Mon, 29 Jun 2020 21:49:01: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:49:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:49:02: #1 tags after filtering in treatment: 23187931 INFO @ Mon, 29 Jun 2020 21:49:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:49:02: #1 finished! INFO @ Mon, 29 Jun 2020 21:49:02: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:49:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:49:03: #2 number of paired peaks: 219 WARNING @ Mon, 29 Jun 2020 21:49:03: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Mon, 29 Jun 2020 21:49:03: start model_add_line... INFO @ Mon, 29 Jun 2020 21:49:03: start X-correlation... INFO @ Mon, 29 Jun 2020 21:49:03: end of X-cor INFO @ Mon, 29 Jun 2020 21:49:03: #2 finished! INFO @ Mon, 29 Jun 2020 21:49:03: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 21:49:03: #2 alternative fragment length(s) may be 1,22,44,541 bps INFO @ Mon, 29 Jun 2020 21:49:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.10_model.r WARNING @ Mon, 29 Jun 2020 21:49:03: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:49:03: #2 You may need to consider one of the other alternative d(s): 1,22,44,541 WARNING @ Mon, 29 Jun 2020 21:49:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:49:03: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:49:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:49:05: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 21:49:09: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:49:10: 21000000 INFO @ Mon, 29 Jun 2020 21:49:14: 22000000 INFO @ Mon, 29 Jun 2020 21:49:19: 23000000 INFO @ Mon, 29 Jun 2020 21:49:20: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 21:49:20: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 21:49:20: #1 total tags in treatment: 23187931 INFO @ Mon, 29 Jun 2020 21:49:20: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:49:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:49:20: #1 tags after filtering in treatment: 23187931 INFO @ Mon, 29 Jun 2020 21:49:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:49:20: #1 finished! INFO @ Mon, 29 Jun 2020 21:49:20: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:49:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:49:22: #2 number of paired peaks: 219 WARNING @ Mon, 29 Jun 2020 21:49:22: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Mon, 29 Jun 2020 21:49:22: start model_add_line... INFO @ Mon, 29 Jun 2020 21:49:22: start X-correlation... INFO @ Mon, 29 Jun 2020 21:49:22: end of X-cor INFO @ Mon, 29 Jun 2020 21:49:22: #2 finished! INFO @ Mon, 29 Jun 2020 21:49:22: #2 predicted fragment length is 1 bps INFO @ Mon, 29 Jun 2020 21:49:22: #2 alternative fragment length(s) may be 1,22,44,541 bps INFO @ Mon, 29 Jun 2020 21:49:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.20_model.r WARNING @ Mon, 29 Jun 2020 21:49:22: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:49:22: #2 You may need to consider one of the other alternative d(s): 1,22,44,541 WARNING @ Mon, 29 Jun 2020 21:49:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:49:22: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:49:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:49:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.05_peaks.xls INFO @ Mon, 29 Jun 2020 21:49:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:49:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.05_summits.bed INFO @ Mon, 29 Jun 2020 21:49:25: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:49:37: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:49:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.10_peaks.xls INFO @ Mon, 29 Jun 2020 21:49:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:49:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.10_summits.bed INFO @ Mon, 29 Jun 2020 21:49:53: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 21:49:55: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:50:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.20_peaks.xls INFO @ Mon, 29 Jun 2020 21:50:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:50:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX172526/SRX172526.20_summits.bed INFO @ Mon, 29 Jun 2020 21:50:11: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling