Job ID = 6367679 SRX = SRX3862418 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:33:05 prefetch.2.10.7: 1) Downloading 'SRR6914655'... 2020-06-15T23:33:05 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:38:02 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:38:02 prefetch.2.10.7: 1) 'SRR6914655' was downloaded successfully 2020-06-15T23:38:02 prefetch.2.10.7: 'SRR6914655' has 0 unresolved dependencies Read 27395908 spots for SRR6914655/SRR6914655.sra Written 27395908 spots for SRR6914655/SRR6914655.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: 00:06:41 27395908 reads; of these: 27395908 (100.00%) were unpaired; of these: 12421039 (45.34%) aligned 0 times 12748599 (46.53%) aligned exactly 1 time 2226270 (8.13%) aligned >1 times 54.66% overall alignment rate Time searching: 00:06:41 Overall time: 00:06:41 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] 14546413 / 14974869 = 0.9714 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 08:48:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.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 08:48:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:54: #1 tag size is determined as 74 bps INFO @ Tue, 16 Jun 2020 08:48:54: #1 tag size = 74 INFO @ Tue, 16 Jun 2020 08:48:54: #1 total tags in treatment: 428456 INFO @ Tue, 16 Jun 2020 08:48:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:54: #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 08:48:54: #1 tags after filtering in treatment: 428456 INFO @ Tue, 16 Jun 2020 08:48:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:54: #2 number of paired peaks: 1540 INFO @ Tue, 16 Jun 2020 08:48:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:54: #2 predicted fragment length is 71 bps INFO @ Tue, 16 Jun 2020 08:48:54: #2 alternative fragment length(s) may be 71,583 bps INFO @ Tue, 16 Jun 2020 08:48:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.05_model.r WARNING @ Tue, 16 Jun 2020 08:48:54: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:48:54: #2 You may need to consider one of the other alternative d(s): 71,583 WARNING @ Tue, 16 Jun 2020 08:48:54: #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 08:48:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:48:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:48:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.05_summits.bed INFO @ Tue, 16 Jun 2020 08:48:55: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (455 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 08:49:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.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 08:49:22: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:22: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:49:24: #1 tag size is determined as 74 bps INFO @ Tue, 16 Jun 2020 08:49:24: #1 tag size = 74 INFO @ Tue, 16 Jun 2020 08:49:24: #1 total tags in treatment: 428456 INFO @ Tue, 16 Jun 2020 08:49:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:24: #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 08:49:24: #1 tags after filtering in treatment: 428456 INFO @ Tue, 16 Jun 2020 08:49:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:24: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:24: #2 number of paired peaks: 1540 INFO @ Tue, 16 Jun 2020 08:49:24: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:24: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:24: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:24: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:24: #2 predicted fragment length is 71 bps INFO @ Tue, 16 Jun 2020 08:49:24: #2 alternative fragment length(s) may be 71,583 bps INFO @ Tue, 16 Jun 2020 08:49:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.10_model.r WARNING @ Tue, 16 Jun 2020 08:49:24: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:49:24: #2 You may need to consider one of the other alternative d(s): 71,583 WARNING @ Tue, 16 Jun 2020 08:49:24: #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 08:49:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:49:25: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.10_summits.bed INFO @ Tue, 16 Jun 2020 08:49:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (205 records, 4 fields): 1 millis CompletedMACS2peakCalling 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 08:49:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.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 08:49:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:49:51: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:49:54: #1 tag size is determined as 74 bps INFO @ Tue, 16 Jun 2020 08:49:54: #1 tag size = 74 INFO @ Tue, 16 Jun 2020 08:49:54: #1 total tags in treatment: 428456 INFO @ Tue, 16 Jun 2020 08:49:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:54: #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 08:49:54: #1 tags after filtering in treatment: 428456 INFO @ Tue, 16 Jun 2020 08:49:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:54: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:54: #2 number of paired peaks: 1540 INFO @ Tue, 16 Jun 2020 08:49:54: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:54: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:54: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:54: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:54: #2 predicted fragment length is 71 bps INFO @ Tue, 16 Jun 2020 08:49:54: #2 alternative fragment length(s) may be 71,583 bps INFO @ Tue, 16 Jun 2020 08:49:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.20_model.r WARNING @ Tue, 16 Jun 2020 08:49:54: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:49:54: #2 You may need to consider one of the other alternative d(s): 71,583 WARNING @ Tue, 16 Jun 2020 08:49:54: #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 08:49:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:49:55: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3862418/SRX3862418.20_summits.bed INFO @ Tue, 16 Jun 2020 08:49:55: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (94 records, 4 fields): 1 millis CompletedMACS2peakCalling