Job ID = 6367674 SRX = SRX3862413 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:28:21 prefetch.2.10.7: 1) Downloading 'SRR6914650'... 2020-06-15T23:28:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:33:43 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:33:43 prefetch.2.10.7: 1) 'SRR6914650' was downloaded successfully 2020-06-15T23:33:43 prefetch.2.10.7: 'SRR6914650' has 0 unresolved dependencies Read 27327585 spots for SRR6914650/SRR6914650.sra Written 27327585 spots for SRR6914650/SRR6914650.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: 00:08:05 27327585 reads; of these: 27327585 (100.00%) were unpaired; of these: 6843411 (25.04%) aligned 0 times 17324670 (63.40%) aligned exactly 1 time 3159504 (11.56%) aligned >1 times 74.96% overall alignment rate Time searching: 00:08:05 Overall time: 00:08:05 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] 19181480 / 20484174 = 0.9364 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 08:47:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.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 08:47:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:47:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:47:59: 1000000 INFO @ Tue, 16 Jun 2020 08:48:00: #1 tag size is determined as 74 bps INFO @ Tue, 16 Jun 2020 08:48:00: #1 tag size = 74 INFO @ Tue, 16 Jun 2020 08:48:00: #1 total tags in treatment: 1302694 INFO @ Tue, 16 Jun 2020 08:48:00: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:00: #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 08:48:01: #1 tags after filtering in treatment: 1302694 INFO @ Tue, 16 Jun 2020 08:48:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:01: #2 number of paired peaks: 1336 INFO @ Tue, 16 Jun 2020 08:48:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:01: #2 predicted fragment length is 70 bps INFO @ Tue, 16 Jun 2020 08:48:01: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 16 Jun 2020 08:48:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.05_model.r WARNING @ Tue, 16 Jun 2020 08:48:01: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:48:01: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 16 Jun 2020 08:48:01: #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 08:48:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:48:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:48:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.05_summits.bed INFO @ Tue, 16 Jun 2020 08:48:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (813 records, 4 fields): 3 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 08:48:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.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 08:48:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:29: 1000000 INFO @ Tue, 16 Jun 2020 08:48:31: #1 tag size is determined as 74 bps INFO @ Tue, 16 Jun 2020 08:48:31: #1 tag size = 74 INFO @ Tue, 16 Jun 2020 08:48:31: #1 total tags in treatment: 1302694 INFO @ Tue, 16 Jun 2020 08:48:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:48:31: #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 08:48:31: #1 tags after filtering in treatment: 1302694 INFO @ Tue, 16 Jun 2020 08:48:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:48:31: #1 finished! INFO @ Tue, 16 Jun 2020 08:48:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:48:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:48:31: #2 number of paired peaks: 1336 INFO @ Tue, 16 Jun 2020 08:48:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:48:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:48:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:48:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:48:31: #2 predicted fragment length is 70 bps INFO @ Tue, 16 Jun 2020 08:48:31: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 16 Jun 2020 08:48:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.10_model.r WARNING @ Tue, 16 Jun 2020 08:48:31: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:48:31: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 16 Jun 2020 08:48:31: #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 08:48:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:48:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:48:34: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:48:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:48:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:48:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.10_summits.bed INFO @ Tue, 16 Jun 2020 08:48:35: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (419 records, 4 fields): 2 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 08:48:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.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 08:48:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:48:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:48:59: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:49:01: #1 tag size is determined as 74 bps INFO @ Tue, 16 Jun 2020 08:49:01: #1 tag size = 74 INFO @ Tue, 16 Jun 2020 08:49:01: #1 total tags in treatment: 1302694 INFO @ Tue, 16 Jun 2020 08:49:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:49:01: #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 08:49:01: #1 tags after filtering in treatment: 1302694 INFO @ Tue, 16 Jun 2020 08:49:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:49:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:49:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:49:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:49:01: #2 number of paired peaks: 1336 INFO @ Tue, 16 Jun 2020 08:49:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:49:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:49:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:49:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:49:01: #2 predicted fragment length is 70 bps INFO @ Tue, 16 Jun 2020 08:49:01: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 16 Jun 2020 08:49:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.20_model.r WARNING @ Tue, 16 Jun 2020 08:49:01: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 08:49:01: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 16 Jun 2020 08:49:01: #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 08:49:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:49:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:49:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:49:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:49:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:49:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3862413/SRX3862413.20_summits.bed INFO @ Tue, 16 Jun 2020 08:49:05: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (215 records, 4 fields): 2 millis CompletedMACS2peakCalling