Job ID = 6366304 SRX = SRX1078728 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:33:06 prefetch.2.10.7: 1) Downloading 'SRR2084335'... 2020-06-15T22:33:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:34:59 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:34:59 prefetch.2.10.7: 1) 'SRR2084335' was downloaded successfully Read 17431794 spots for SRR2084335/SRR2084335.sra Written 17431794 spots for SRR2084335/SRR2084335.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: 00:04:12 17431794 reads; of these: 17431794 (100.00%) were unpaired; of these: 234678 (1.35%) aligned 0 times 14452582 (82.91%) aligned exactly 1 time 2744534 (15.74%) aligned >1 times 98.65% overall alignment rate Time searching: 00:04:12 Overall time: 00:04:12 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] 3133566 / 17197116 = 0.1822 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 07:44:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.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 07:44:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:44:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:45:05: 1000000 INFO @ Tue, 16 Jun 2020 07:45:12: 2000000 INFO @ Tue, 16 Jun 2020 07:45:20: 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 07:45:27: 4000000 INFO @ Tue, 16 Jun 2020 07:45:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.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 07:45:28: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:45:28: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:45:34: 5000000 INFO @ Tue, 16 Jun 2020 07:45:36: 1000000 INFO @ Tue, 16 Jun 2020 07:45:41: 6000000 INFO @ Tue, 16 Jun 2020 07:45:43: 2000000 INFO @ Tue, 16 Jun 2020 07:45:49: 7000000 INFO @ Tue, 16 Jun 2020 07:45:50: 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 07:45:56: 8000000 INFO @ Tue, 16 Jun 2020 07:45:57: 4000000 INFO @ Tue, 16 Jun 2020 07:45:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.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 07:45:58: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:45:58: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:46:04: 9000000 INFO @ Tue, 16 Jun 2020 07:46:04: 5000000 INFO @ Tue, 16 Jun 2020 07:46:06: 1000000 INFO @ Tue, 16 Jun 2020 07:46:11: 10000000 INFO @ Tue, 16 Jun 2020 07:46:12: 6000000 INFO @ Tue, 16 Jun 2020 07:46:13: 2000000 INFO @ Tue, 16 Jun 2020 07:46:18: 11000000 INFO @ Tue, 16 Jun 2020 07:46:19: 7000000 INFO @ Tue, 16 Jun 2020 07:46:20: 3000000 INFO @ Tue, 16 Jun 2020 07:46:26: 8000000 INFO @ Tue, 16 Jun 2020 07:46:26: 12000000 INFO @ Tue, 16 Jun 2020 07:46:27: 4000000 INFO @ Tue, 16 Jun 2020 07:46:33: 9000000 INFO @ Tue, 16 Jun 2020 07:46:33: 13000000 INFO @ Tue, 16 Jun 2020 07:46:34: 5000000 INFO @ Tue, 16 Jun 2020 07:46:40: 10000000 INFO @ Tue, 16 Jun 2020 07:46:41: 14000000 INFO @ Tue, 16 Jun 2020 07:46:41: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:46:41: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:46:41: #1 total tags in treatment: 14063550 INFO @ Tue, 16 Jun 2020 07:46:41: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:46:41: #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 07:46:41: 6000000 INFO @ Tue, 16 Jun 2020 07:46:41: #1 tags after filtering in treatment: 14063550 INFO @ Tue, 16 Jun 2020 07:46:41: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:46:41: #1 finished! INFO @ Tue, 16 Jun 2020 07:46:41: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:46:41: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:46:42: #2 number of paired peaks: 322 WARNING @ Tue, 16 Jun 2020 07:46:42: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Tue, 16 Jun 2020 07:46:42: start model_add_line... INFO @ Tue, 16 Jun 2020 07:46:42: start X-correlation... INFO @ Tue, 16 Jun 2020 07:46:42: end of X-cor INFO @ Tue, 16 Jun 2020 07:46:42: #2 finished! INFO @ Tue, 16 Jun 2020 07:46:42: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 07:46:42: #2 alternative fragment length(s) may be 1,44,521,560 bps INFO @ Tue, 16 Jun 2020 07:46:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.05_model.r WARNING @ Tue, 16 Jun 2020 07:46:42: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:46:42: #2 You may need to consider one of the other alternative d(s): 1,44,521,560 WARNING @ Tue, 16 Jun 2020 07:46:42: #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 07:46:42: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:46:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:46:47: 11000000 INFO @ Tue, 16 Jun 2020 07:46:48: 7000000 INFO @ Tue, 16 Jun 2020 07:46:53: 12000000 INFO @ Tue, 16 Jun 2020 07:46:55: 8000000 INFO @ Tue, 16 Jun 2020 07:47:00: 13000000 INFO @ Tue, 16 Jun 2020 07:47:01: 9000000 INFO @ Tue, 16 Jun 2020 07:47:07: 14000000 INFO @ Tue, 16 Jun 2020 07:47:07: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:47:07: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:47:07: #1 total tags in treatment: 14063550 INFO @ Tue, 16 Jun 2020 07:47:07: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:47:07: #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 07:47:08: #1 tags after filtering in treatment: 14063550 INFO @ Tue, 16 Jun 2020 07:47:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:47:08: #1 finished! INFO @ Tue, 16 Jun 2020 07:47:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:47:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:47:08: 10000000 INFO @ Tue, 16 Jun 2020 07:47:09: #2 number of paired peaks: 322 WARNING @ Tue, 16 Jun 2020 07:47:09: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Tue, 16 Jun 2020 07:47:09: start model_add_line... INFO @ Tue, 16 Jun 2020 07:47:09: start X-correlation... INFO @ Tue, 16 Jun 2020 07:47:09: end of X-cor INFO @ Tue, 16 Jun 2020 07:47:09: #2 finished! INFO @ Tue, 16 Jun 2020 07:47:09: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 07:47:09: #2 alternative fragment length(s) may be 1,44,521,560 bps INFO @ Tue, 16 Jun 2020 07:47:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.10_model.r WARNING @ Tue, 16 Jun 2020 07:47:09: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:47:09: #2 You may need to consider one of the other alternative d(s): 1,44,521,560 WARNING @ Tue, 16 Jun 2020 07:47:09: #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 07:47:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:47:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:47:09: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:47:14: 11000000 INFO @ Tue, 16 Jun 2020 07:47:20: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:47:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:47:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:47:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.05_summits.bed INFO @ Tue, 16 Jun 2020 07:47:23: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (724 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:47:27: 13000000 INFO @ Tue, 16 Jun 2020 07:47:33: 14000000 INFO @ Tue, 16 Jun 2020 07:47:33: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 07:47:33: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 07:47:33: #1 total tags in treatment: 14063550 INFO @ Tue, 16 Jun 2020 07:47:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:47:33: #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 07:47:33: #1 tags after filtering in treatment: 14063550 INFO @ Tue, 16 Jun 2020 07:47:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:47:33: #1 finished! INFO @ Tue, 16 Jun 2020 07:47:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:47:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:47:34: #2 number of paired peaks: 322 WARNING @ Tue, 16 Jun 2020 07:47:34: Fewer paired peaks (322) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 322 pairs to build model! INFO @ Tue, 16 Jun 2020 07:47:34: start model_add_line... INFO @ Tue, 16 Jun 2020 07:47:35: start X-correlation... INFO @ Tue, 16 Jun 2020 07:47:35: end of X-cor INFO @ Tue, 16 Jun 2020 07:47:35: #2 finished! INFO @ Tue, 16 Jun 2020 07:47:35: #2 predicted fragment length is 44 bps INFO @ Tue, 16 Jun 2020 07:47:35: #2 alternative fragment length(s) may be 1,44,521,560 bps INFO @ Tue, 16 Jun 2020 07:47:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.20_model.r WARNING @ Tue, 16 Jun 2020 07:47:35: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:47:35: #2 You may need to consider one of the other alternative d(s): 1,44,521,560 WARNING @ Tue, 16 Jun 2020 07:47:35: #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 07:47:35: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:47:35: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:47:36: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:47:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:47:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:47:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.10_summits.bed INFO @ Tue, 16 Jun 2020 07:47:50: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (480 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:48:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:48:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:48:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:48:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1078728/SRX1078728.20_summits.bed INFO @ Tue, 16 Jun 2020 07:48:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (164 records, 4 fields): 2 millis CompletedMACS2peakCalling