Job ID = 6366551 SRX = SRX188617 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:49:57 prefetch.2.10.7: 1) Downloading 'SRR573728'... 2020-06-15T22:49:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:50:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:50:23 prefetch.2.10.7: 'SRR573728' is valid 2020-06-15T22:50:23 prefetch.2.10.7: 1) 'SRR573728' was downloaded successfully Read 2867660 spots for SRR573728/SRR573728.sra Written 2867660 spots for SRR573728/SRR573728.sra 2020-06-15T22:50:42 prefetch.2.10.7: 1) Downloading 'SRR573729'... 2020-06-15T22:50:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:51:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:51:06 prefetch.2.10.7: 'SRR573729' is valid 2020-06-15T22:51:06 prefetch.2.10.7: 1) 'SRR573729' was downloaded successfully Read 2054866 spots for SRR573729/SRR573729.sra Written 2054866 spots for SRR573729/SRR573729.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: 00:00:31 4922526 reads; of these: 4922526 (100.00%) were unpaired; of these: 2877040 (58.45%) aligned 0 times 1829331 (37.16%) aligned exactly 1 time 216155 (4.39%) aligned >1 times 41.55% overall alignment rate Time searching: 00:00:31 Overall time: 00:00:31 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] 155918 / 2045486 = 0.0762 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 07:52:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.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 07:52:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:52:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:52:57: 1000000 INFO @ Tue, 16 Jun 2020 07:53:02: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:53:02: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:53:02: #1 total tags in treatment: 1889568 INFO @ Tue, 16 Jun 2020 07:53:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:02: #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 07:53:02: #1 tags after filtering in treatment: 1889568 INFO @ Tue, 16 Jun 2020 07:53:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:02: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:03: #2 number of paired peaks: 3118 INFO @ Tue, 16 Jun 2020 07:53:03: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:03: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:03: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:03: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:03: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 07:53:03: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 16 Jun 2020 07:53:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.05_model.r INFO @ Tue, 16 Jun 2020 07:53:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:53:08: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.05_summits.bed INFO @ Tue, 16 Jun 2020 07:53:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1668 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 07:53:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.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 07:53:21: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:21: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:26: 1000000 INFO @ Tue, 16 Jun 2020 07:53:31: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:53:31: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:53:31: #1 total tags in treatment: 1889568 INFO @ Tue, 16 Jun 2020 07:53:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:53:31: #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 07:53:31: #1 tags after filtering in treatment: 1889568 INFO @ Tue, 16 Jun 2020 07:53:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:53:31: #1 finished! INFO @ Tue, 16 Jun 2020 07:53:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:53:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:53:31: #2 number of paired peaks: 3118 INFO @ Tue, 16 Jun 2020 07:53:31: start model_add_line... INFO @ Tue, 16 Jun 2020 07:53:31: start X-correlation... INFO @ Tue, 16 Jun 2020 07:53:31: end of X-cor INFO @ Tue, 16 Jun 2020 07:53:31: #2 finished! INFO @ Tue, 16 Jun 2020 07:53:31: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 07:53:31: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 16 Jun 2020 07:53:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.10_model.r INFO @ Tue, 16 Jun 2020 07:53:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:53:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:53:37: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:53:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:53:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:53:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.10_summits.bed INFO @ Tue, 16 Jun 2020 07:53:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (508 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 07:53:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.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 07:53:51: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:53:51: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:53:56: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:54:01: #1 tag size is determined as 32 bps INFO @ Tue, 16 Jun 2020 07:54:01: #1 tag size = 32 INFO @ Tue, 16 Jun 2020 07:54:01: #1 total tags in treatment: 1889568 INFO @ Tue, 16 Jun 2020 07:54:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:54:01: #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 07:54:01: #1 tags after filtering in treatment: 1889568 INFO @ Tue, 16 Jun 2020 07:54:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:54:01: #1 finished! INFO @ Tue, 16 Jun 2020 07:54:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:54:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:54:01: #2 number of paired peaks: 3118 INFO @ Tue, 16 Jun 2020 07:54:01: start model_add_line... INFO @ Tue, 16 Jun 2020 07:54:01: start X-correlation... INFO @ Tue, 16 Jun 2020 07:54:01: end of X-cor INFO @ Tue, 16 Jun 2020 07:54:01: #2 finished! INFO @ Tue, 16 Jun 2020 07:54:01: #2 predicted fragment length is 153 bps INFO @ Tue, 16 Jun 2020 07:54:01: #2 alternative fragment length(s) may be 153 bps INFO @ Tue, 16 Jun 2020 07:54:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.20_model.r INFO @ Tue, 16 Jun 2020 07:54:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:54:01: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:54:07: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:54:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:54:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:54:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX188617/SRX188617.20_summits.bed INFO @ Tue, 16 Jun 2020 07:54:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (142 records, 4 fields): 2 millis CompletedMACS2peakCalling