Job ID = 6366558 SRX = SRX1936236 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:01:38 prefetch.2.10.7: 1) Downloading 'SRR3879842'... 2020-06-15T23:01:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:03:09 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:03:09 prefetch.2.10.7: 1) 'SRR3879842' was downloaded successfully Read 24704893 spots for SRR3879842/SRR3879842.sra Written 24704893 spots for SRR3879842/SRR3879842.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: 00:06:01 24704893 reads; of these: 24704893 (100.00%) were unpaired; of these: 1155471 (4.68%) aligned 0 times 19676161 (79.64%) aligned exactly 1 time 3873261 (15.68%) aligned >1 times 95.32% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 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] 3589463 / 23549422 = 0.1524 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 08:16:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.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 08:16:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:16:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:16:19: 1000000 INFO @ Tue, 16 Jun 2020 08:16:26: 2000000 INFO @ Tue, 16 Jun 2020 08:16:33: 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 08:16:40: 4000000 INFO @ Tue, 16 Jun 2020 08:16:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.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 08:16:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:16:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:16:48: 5000000 INFO @ Tue, 16 Jun 2020 08:16:49: 1000000 INFO @ Tue, 16 Jun 2020 08:16:55: 6000000 INFO @ Tue, 16 Jun 2020 08:16:57: 2000000 INFO @ Tue, 16 Jun 2020 08:17:03: 7000000 INFO @ Tue, 16 Jun 2020 08:17:04: 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 08:17:11: 8000000 INFO @ Tue, 16 Jun 2020 08:17:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.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 08:17:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:17:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:17:12: 4000000 INFO @ Tue, 16 Jun 2020 08:17:18: 1000000 INFO @ Tue, 16 Jun 2020 08:17:19: 9000000 INFO @ Tue, 16 Jun 2020 08:17:20: 5000000 INFO @ Tue, 16 Jun 2020 08:17:25: 2000000 INFO @ Tue, 16 Jun 2020 08:17:27: 10000000 INFO @ Tue, 16 Jun 2020 08:17:27: 6000000 INFO @ Tue, 16 Jun 2020 08:17:32: 3000000 INFO @ Tue, 16 Jun 2020 08:17:34: 11000000 INFO @ Tue, 16 Jun 2020 08:17:35: 7000000 INFO @ Tue, 16 Jun 2020 08:17:39: 4000000 INFO @ Tue, 16 Jun 2020 08:17:42: 12000000 INFO @ Tue, 16 Jun 2020 08:17:43: 8000000 INFO @ Tue, 16 Jun 2020 08:17:46: 5000000 INFO @ Tue, 16 Jun 2020 08:17:50: 13000000 INFO @ Tue, 16 Jun 2020 08:17:50: 9000000 INFO @ Tue, 16 Jun 2020 08:17:54: 6000000 INFO @ Tue, 16 Jun 2020 08:17:58: 14000000 INFO @ Tue, 16 Jun 2020 08:17:58: 10000000 INFO @ Tue, 16 Jun 2020 08:18:01: 7000000 INFO @ Tue, 16 Jun 2020 08:18:05: 15000000 INFO @ Tue, 16 Jun 2020 08:18:06: 11000000 INFO @ Tue, 16 Jun 2020 08:18:08: 8000000 INFO @ Tue, 16 Jun 2020 08:18:13: 16000000 INFO @ Tue, 16 Jun 2020 08:18:13: 12000000 INFO @ Tue, 16 Jun 2020 08:18:15: 9000000 INFO @ Tue, 16 Jun 2020 08:18:21: 13000000 INFO @ Tue, 16 Jun 2020 08:18:21: 17000000 INFO @ Tue, 16 Jun 2020 08:18:22: 10000000 INFO @ Tue, 16 Jun 2020 08:18:28: 14000000 INFO @ Tue, 16 Jun 2020 08:18:28: 18000000 INFO @ Tue, 16 Jun 2020 08:18:29: 11000000 INFO @ Tue, 16 Jun 2020 08:18:36: 12000000 INFO @ Tue, 16 Jun 2020 08:18:36: 15000000 INFO @ Tue, 16 Jun 2020 08:18:36: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:18:43: 13000000 INFO @ Tue, 16 Jun 2020 08:18:43: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:18:43: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:18:43: #1 total tags in treatment: 19959959 INFO @ Tue, 16 Jun 2020 08:18:43: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:18:43: #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 08:18:43: 16000000 INFO @ Tue, 16 Jun 2020 08:18:44: #1 tags after filtering in treatment: 19959959 INFO @ Tue, 16 Jun 2020 08:18:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:18:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:18:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:18:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:18:45: #2 number of paired peaks: 201 WARNING @ Tue, 16 Jun 2020 08:18:45: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Tue, 16 Jun 2020 08:18:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:18:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:18:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:18:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:18:45: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:18:45: #2 alternative fragment length(s) may be 1,37 bps INFO @ Tue, 16 Jun 2020 08:18:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.05_model.r WARNING @ Tue, 16 Jun 2020 08:18:45: #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 08:18:45: #2 You may need to consider one of the other alternative d(s): 1,37 WARNING @ Tue, 16 Jun 2020 08:18:45: #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 08:18:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:18:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:18:49: 14000000 INFO @ Tue, 16 Jun 2020 08:18:51: 17000000 INFO @ Tue, 16 Jun 2020 08:18:56: 15000000 INFO @ Tue, 16 Jun 2020 08:18:58: 18000000 INFO @ Tue, 16 Jun 2020 08:19:03: 16000000 INFO @ Tue, 16 Jun 2020 08:19:06: 19000000 INFO @ Tue, 16 Jun 2020 08:19:10: 17000000 INFO @ Tue, 16 Jun 2020 08:19:13: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:19:13: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:19:13: #1 total tags in treatment: 19959959 INFO @ Tue, 16 Jun 2020 08:19:13: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:13: #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 08:19:13: #1 tags after filtering in treatment: 19959959 INFO @ Tue, 16 Jun 2020 08:19:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:13: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:13: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:15: #2 number of paired peaks: 201 WARNING @ Tue, 16 Jun 2020 08:19:15: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:15: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:15: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:15: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:15: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:15: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:19:15: #2 alternative fragment length(s) may be 1,37 bps INFO @ Tue, 16 Jun 2020 08:19:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.10_model.r WARNING @ Tue, 16 Jun 2020 08:19:15: #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 08:19:15: #2 You may need to consider one of the other alternative d(s): 1,37 WARNING @ Tue, 16 Jun 2020 08:19:15: #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 08:19:15: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:19:17: 18000000 INFO @ Tue, 16 Jun 2020 08:19:18: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:19:23: 19000000 INFO @ Tue, 16 Jun 2020 08:19:29: #1 tag size is determined as 52 bps INFO @ Tue, 16 Jun 2020 08:19:29: #1 tag size = 52 INFO @ Tue, 16 Jun 2020 08:19:29: #1 total tags in treatment: 19959959 INFO @ Tue, 16 Jun 2020 08:19:29: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:19:29: #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 08:19:29: #1 tags after filtering in treatment: 19959959 INFO @ Tue, 16 Jun 2020 08:19:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:19:29: #1 finished! INFO @ Tue, 16 Jun 2020 08:19:29: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:19:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:19:31: #2 number of paired peaks: 201 WARNING @ Tue, 16 Jun 2020 08:19:31: Fewer paired peaks (201) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 201 pairs to build model! INFO @ Tue, 16 Jun 2020 08:19:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:19:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:19:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:19:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:19:31: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:19:31: #2 alternative fragment length(s) may be 1,37 bps INFO @ Tue, 16 Jun 2020 08:19:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.20_model.r WARNING @ Tue, 16 Jun 2020 08:19:31: #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 08:19:31: #2 You may need to consider one of the other alternative d(s): 1,37 WARNING @ Tue, 16 Jun 2020 08:19:31: #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 08:19:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:19:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:19:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:19:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:19:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.05_summits.bed INFO @ Tue, 16 Jun 2020 08:19:34: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:19:48: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:03: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:20:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.10_summits.bed INFO @ Tue, 16 Jun 2020 08:20:04: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:20:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:20:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:20:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1936236/SRX1936236.20_summits.bed INFO @ Tue, 16 Jun 2020 08:20:19: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling