Job ID = 6366201 SRX = SRX065726 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:47:52 prefetch.2.10.7: 1) Downloading 'SRR217432'... 2020-06-15T22:47:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:48:33 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:48:34 prefetch.2.10.7: 'SRR217432' is valid 2020-06-15T22:48:34 prefetch.2.10.7: 1) 'SRR217432' was downloaded successfully Read 8990633 spots for SRR217432/SRR217432.sra Written 8990633 spots for SRR217432/SRR217432.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: 00:00:01 Multiseed full-index search: 00:00:57 8990633 reads; of these: 8990633 (100.00%) were unpaired; of these: 4598502 (51.15%) aligned 0 times 3673048 (40.85%) aligned exactly 1 time 719083 (8.00%) aligned >1 times 48.85% overall alignment rate Time searching: 00:00:58 Overall time: 00:00:58 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_rmdupse_core] 475553 / 4392131 = 0.1083 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 07:51:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.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 07:51:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:51:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:51:37: 1000000 INFO @ Tue, 16 Jun 2020 07:51:43: 2000000 INFO @ Tue, 16 Jun 2020 07:51:48: 3000000 INFO @ Tue, 16 Jun 2020 07:51:53: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:51:53: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:51:53: #1 total tags in treatment: 3916578 INFO @ Tue, 16 Jun 2020 07:51:53: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:51:53: #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 07:51:53: #1 tags after filtering in treatment: 3916578 INFO @ Tue, 16 Jun 2020 07:51:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:51:53: #1 finished! INFO @ Tue, 16 Jun 2020 07:51:53: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:51:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:51:54: #2 number of paired peaks: 477 WARNING @ Tue, 16 Jun 2020 07:51:54: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Tue, 16 Jun 2020 07:51:54: start model_add_line... INFO @ Tue, 16 Jun 2020 07:51:54: start X-correlation... INFO @ Tue, 16 Jun 2020 07:51:54: end of X-cor INFO @ Tue, 16 Jun 2020 07:51:54: #2 finished! INFO @ Tue, 16 Jun 2020 07:51:54: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 07:51:54: #2 alternative fragment length(s) may be 3,34,503,587 bps INFO @ Tue, 16 Jun 2020 07:51:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.05_model.r WARNING @ Tue, 16 Jun 2020 07:51:54: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:51:54: #2 You may need to consider one of the other alternative d(s): 3,34,503,587 WARNING @ Tue, 16 Jun 2020 07:51:54: #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 07:51:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:51:54: #3 Pre-compute pvalue-qvalue table... 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 07:52:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:52:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.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 07:52:01: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:01: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:52:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:52:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:52:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.05_summits.bed INFO @ Tue, 16 Jun 2020 07:52:05: Done! INFO @ Tue, 16 Jun 2020 07:52:06: 1000000 pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (417 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:52:10: 2000000 INFO @ Tue, 16 Jun 2020 07:52:15: 3000000 INFO @ Tue, 16 Jun 2020 07:52:19: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:52:19: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:52:19: #1 total tags in treatment: 3916578 INFO @ Tue, 16 Jun 2020 07:52:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:19: #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 07:52:19: #1 tags after filtering in treatment: 3916578 INFO @ Tue, 16 Jun 2020 07:52:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:19: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:19: #2 number of paired peaks: 477 WARNING @ Tue, 16 Jun 2020 07:52:19: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Tue, 16 Jun 2020 07:52:19: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:19: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:19: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:19: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:19: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 07:52:19: #2 alternative fragment length(s) may be 3,34,503,587 bps INFO @ Tue, 16 Jun 2020 07:52:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.10_model.r WARNING @ Tue, 16 Jun 2020 07:52:20: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:52:20: #2 You may need to consider one of the other alternative d(s): 3,34,503,587 WARNING @ Tue, 16 Jun 2020 07:52:20: #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 07:52:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:52:27: #3 Call peaks for each chromosome... 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 07:52:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:52:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:52:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.10_summits.bed INFO @ Tue, 16 Jun 2020 07:52:31: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (201 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 07:52:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.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 07:52:31: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:31: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:52:36: 1000000 INFO @ Tue, 16 Jun 2020 07:52:40: 2000000 INFO @ Tue, 16 Jun 2020 07:52:45: 3000000 INFO @ Tue, 16 Jun 2020 07:52:49: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:52:49: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:52:49: #1 total tags in treatment: 3916578 INFO @ Tue, 16 Jun 2020 07:52:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:52:49: #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 07:52:49: #1 tags after filtering in treatment: 3916578 INFO @ Tue, 16 Jun 2020 07:52:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:52:49: #1 finished! INFO @ Tue, 16 Jun 2020 07:52:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:52:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:52:49: #2 number of paired peaks: 477 WARNING @ Tue, 16 Jun 2020 07:52:49: Fewer paired peaks (477) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 477 pairs to build model! INFO @ Tue, 16 Jun 2020 07:52:49: start model_add_line... INFO @ Tue, 16 Jun 2020 07:52:50: start X-correlation... INFO @ Tue, 16 Jun 2020 07:52:50: end of X-cor INFO @ Tue, 16 Jun 2020 07:52:50: #2 finished! INFO @ Tue, 16 Jun 2020 07:52:50: #2 predicted fragment length is 34 bps INFO @ Tue, 16 Jun 2020 07:52:50: #2 alternative fragment length(s) may be 3,34,503,587 bps INFO @ Tue, 16 Jun 2020 07:52:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.20_model.r WARNING @ Tue, 16 Jun 2020 07:52:50: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 07:52:50: #2 You may need to consider one of the other alternative d(s): 3,34,503,587 WARNING @ Tue, 16 Jun 2020 07:52:50: #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 07:52:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:52:50: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:52:57: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX065726/SRX065726.20_summits.bed INFO @ Tue, 16 Jun 2020 07:53:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (48 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。