Job ID = 6366506 SRX = SRX1674086 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:46:07 prefetch.2.10.7: 1) Downloading 'SRR3320132'... 2020-06-15T22:46:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:54:07 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:54:07 prefetch.2.10.7: 1) 'SRR3320132' was downloaded successfully Read 86067449 spots for SRR3320132/SRR3320132.sra Written 86067449 spots for SRR3320132/SRR3320132.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: 00:19:33 86067449 reads; of these: 86067449 (100.00%) were unpaired; of these: 9165994 (10.65%) aligned 0 times 65248512 (75.81%) aligned exactly 1 time 11652943 (13.54%) aligned >1 times 89.35% overall alignment rate Time searching: 00:19:33 Overall time: 00:19:33 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 32 files... [bam_rmdupse_core] 49019475 / 76901455 = 0.6374 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 08:34:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.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 08:34:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:08: 1000000 INFO @ Tue, 16 Jun 2020 08:34:16: 2000000 INFO @ Tue, 16 Jun 2020 08:34:23: 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 08:34:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.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 08:34:30: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:34:30: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:34:31: 4000000 INFO @ Tue, 16 Jun 2020 08:34:38: 1000000 INFO @ Tue, 16 Jun 2020 08:34:38: 5000000 INFO @ Tue, 16 Jun 2020 08:34:45: 2000000 INFO @ Tue, 16 Jun 2020 08:34:46: 6000000 INFO @ Tue, 16 Jun 2020 08:34:53: 3000000 INFO @ Tue, 16 Jun 2020 08:34:53: 7000000 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 08:35:00: 4000000 INFO @ Tue, 16 Jun 2020 08:35:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.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 08:35:00: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:35:00: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:35:01: 8000000 INFO @ Tue, 16 Jun 2020 08:35:07: 1000000 INFO @ Tue, 16 Jun 2020 08:35:08: 5000000 INFO @ Tue, 16 Jun 2020 08:35:08: 9000000 INFO @ Tue, 16 Jun 2020 08:35:14: 2000000 INFO @ Tue, 16 Jun 2020 08:35:15: 6000000 INFO @ Tue, 16 Jun 2020 08:35:16: 10000000 INFO @ Tue, 16 Jun 2020 08:35:20: 3000000 INFO @ Tue, 16 Jun 2020 08:35:23: 7000000 INFO @ Tue, 16 Jun 2020 08:35:23: 11000000 INFO @ Tue, 16 Jun 2020 08:35:27: 4000000 INFO @ Tue, 16 Jun 2020 08:35:30: 8000000 INFO @ Tue, 16 Jun 2020 08:35:31: 12000000 INFO @ Tue, 16 Jun 2020 08:35:33: 5000000 INFO @ Tue, 16 Jun 2020 08:35:38: 9000000 INFO @ Tue, 16 Jun 2020 08:35:38: 13000000 INFO @ Tue, 16 Jun 2020 08:35:40: 6000000 INFO @ Tue, 16 Jun 2020 08:35:46: 14000000 INFO @ Tue, 16 Jun 2020 08:35:46: 10000000 INFO @ Tue, 16 Jun 2020 08:35:46: 7000000 INFO @ Tue, 16 Jun 2020 08:35:53: 8000000 INFO @ Tue, 16 Jun 2020 08:35:53: 15000000 INFO @ Tue, 16 Jun 2020 08:35:53: 11000000 INFO @ Tue, 16 Jun 2020 08:36:00: 9000000 INFO @ Tue, 16 Jun 2020 08:36:01: 16000000 INFO @ Tue, 16 Jun 2020 08:36:01: 12000000 INFO @ Tue, 16 Jun 2020 08:36:06: 10000000 INFO @ Tue, 16 Jun 2020 08:36:08: 17000000 INFO @ Tue, 16 Jun 2020 08:36:08: 13000000 INFO @ Tue, 16 Jun 2020 08:36:13: 11000000 INFO @ Tue, 16 Jun 2020 08:36:16: 18000000 INFO @ Tue, 16 Jun 2020 08:36:16: 14000000 INFO @ Tue, 16 Jun 2020 08:36:20: 12000000 INFO @ Tue, 16 Jun 2020 08:36:23: 19000000 INFO @ Tue, 16 Jun 2020 08:36:24: 15000000 INFO @ Tue, 16 Jun 2020 08:36:26: 13000000 INFO @ Tue, 16 Jun 2020 08:36:30: 20000000 INFO @ Tue, 16 Jun 2020 08:36:32: 16000000 INFO @ Tue, 16 Jun 2020 08:36:33: 14000000 INFO @ Tue, 16 Jun 2020 08:36:37: 21000000 INFO @ Tue, 16 Jun 2020 08:36:40: 17000000 INFO @ Tue, 16 Jun 2020 08:36:40: 15000000 INFO @ Tue, 16 Jun 2020 08:36:43: 22000000 INFO @ Tue, 16 Jun 2020 08:36:47: 16000000 INFO @ Tue, 16 Jun 2020 08:36:47: 18000000 INFO @ Tue, 16 Jun 2020 08:36:50: 23000000 INFO @ Tue, 16 Jun 2020 08:36:53: 17000000 INFO @ Tue, 16 Jun 2020 08:36:55: 19000000 INFO @ Tue, 16 Jun 2020 08:36:57: 24000000 INFO @ Tue, 16 Jun 2020 08:37:00: 18000000 INFO @ Tue, 16 Jun 2020 08:37:03: 20000000 INFO @ Tue, 16 Jun 2020 08:37:04: 25000000 INFO @ Tue, 16 Jun 2020 08:37:07: 19000000 INFO @ Tue, 16 Jun 2020 08:37:10: 26000000 INFO @ Tue, 16 Jun 2020 08:37:10: 21000000 INFO @ Tue, 16 Jun 2020 08:37:14: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:37:17: 27000000 INFO @ Tue, 16 Jun 2020 08:37:18: 22000000 INFO @ Tue, 16 Jun 2020 08:37:20: 21000000 INFO @ Tue, 16 Jun 2020 08:37:23: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:37:23: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:37:23: #1 total tags in treatment: 27881980 INFO @ Tue, 16 Jun 2020 08:37:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:37:23: #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 08:37:24: #1 tags after filtering in treatment: 27881980 INFO @ Tue, 16 Jun 2020 08:37:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:37:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:37:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:37:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:37:25: 23000000 INFO @ Tue, 16 Jun 2020 08:37:26: #2 number of paired peaks: 187 WARNING @ Tue, 16 Jun 2020 08:37:26: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Tue, 16 Jun 2020 08:37:26: start model_add_line... INFO @ Tue, 16 Jun 2020 08:37:26: start X-correlation... INFO @ Tue, 16 Jun 2020 08:37:26: end of X-cor INFO @ Tue, 16 Jun 2020 08:37:26: #2 finished! INFO @ Tue, 16 Jun 2020 08:37:26: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:37:26: #2 alternative fragment length(s) may be 1,14,39,583 bps INFO @ Tue, 16 Jun 2020 08:37:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.05_model.r WARNING @ Tue, 16 Jun 2020 08:37:26: #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 08:37:26: #2 You may need to consider one of the other alternative d(s): 1,14,39,583 WARNING @ Tue, 16 Jun 2020 08:37:26: #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 08:37:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:37:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:37:27: 22000000 INFO @ Tue, 16 Jun 2020 08:37:33: 24000000 INFO @ Tue, 16 Jun 2020 08:37:33: 23000000 INFO @ Tue, 16 Jun 2020 08:37:40: 24000000 INFO @ Tue, 16 Jun 2020 08:37:40: 25000000 INFO @ Tue, 16 Jun 2020 08:37:46: 25000000 INFO @ Tue, 16 Jun 2020 08:37:48: 26000000 INFO @ Tue, 16 Jun 2020 08:37:53: 26000000 INFO @ Tue, 16 Jun 2020 08:37:56: 27000000 INFO @ Tue, 16 Jun 2020 08:37:59: 27000000 INFO @ Tue, 16 Jun 2020 08:38:02: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:38:02: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:38:02: #1 total tags in treatment: 27881980 INFO @ Tue, 16 Jun 2020 08:38:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:38:02: #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 08:38:03: #1 tags after filtering in treatment: 27881980 INFO @ Tue, 16 Jun 2020 08:38:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:38:03: #1 finished! INFO @ Tue, 16 Jun 2020 08:38:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:38:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:38:05: #2 number of paired peaks: 187 WARNING @ Tue, 16 Jun 2020 08:38:05: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Tue, 16 Jun 2020 08:38:05: start model_add_line... INFO @ Tue, 16 Jun 2020 08:38:05: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:38:05: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:38:05: #1 total tags in treatment: 27881980 INFO @ Tue, 16 Jun 2020 08:38:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:38:05: #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 08:38:05: start X-correlation... INFO @ Tue, 16 Jun 2020 08:38:05: end of X-cor INFO @ Tue, 16 Jun 2020 08:38:05: #2 finished! INFO @ Tue, 16 Jun 2020 08:38:05: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:38:05: #2 alternative fragment length(s) may be 1,14,39,583 bps INFO @ Tue, 16 Jun 2020 08:38:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.10_model.r WARNING @ Tue, 16 Jun 2020 08:38:05: #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 08:38:05: #2 You may need to consider one of the other alternative d(s): 1,14,39,583 WARNING @ Tue, 16 Jun 2020 08:38:05: #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 08:38:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:38:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:38:05: #1 tags after filtering in treatment: 27881980 INFO @ Tue, 16 Jun 2020 08:38:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:38:05: #1 finished! INFO @ Tue, 16 Jun 2020 08:38:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:38:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:38:06: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:38:07: #2 number of paired peaks: 187 WARNING @ Tue, 16 Jun 2020 08:38:07: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Tue, 16 Jun 2020 08:38:07: start model_add_line... INFO @ Tue, 16 Jun 2020 08:38:07: start X-correlation... INFO @ Tue, 16 Jun 2020 08:38:07: end of X-cor INFO @ Tue, 16 Jun 2020 08:38:07: #2 finished! INFO @ Tue, 16 Jun 2020 08:38:07: #2 predicted fragment length is 1 bps INFO @ Tue, 16 Jun 2020 08:38:07: #2 alternative fragment length(s) may be 1,14,39,583 bps INFO @ Tue, 16 Jun 2020 08:38:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.20_model.r WARNING @ Tue, 16 Jun 2020 08:38:08: #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 08:38:08: #2 You may need to consider one of the other alternative d(s): 1,14,39,583 WARNING @ Tue, 16 Jun 2020 08:38:08: #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 08:38:08: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:38:08: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:38:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:38:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:38:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.05_summits.bed INFO @ Tue, 16 Jun 2020 08:38:26: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:38:46: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:38:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:39:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:39:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:39:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.10_summits.bed INFO @ Tue, 16 Jun 2020 08:39:05: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:39:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:39:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:39:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1674086/SRX1674086.20_summits.bed INFO @ Tue, 16 Jun 2020 08:39:06: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling