Job ID = 6368778 SRX = SRX560682 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:31:42 prefetch.2.10.7: 1) Downloading 'SRR1314159'... 2020-06-16T00:31:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:32:38 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:32:38 prefetch.2.10.7: 'SRR1314159' is valid 2020-06-16T00:32:38 prefetch.2.10.7: 1) 'SRR1314159' was downloaded successfully 2020-06-16T00:32:38 prefetch.2.10.7: 'SRR1314159' has 0 unresolved dependencies Read 4000000 spots for SRR1314159/SRR1314159.sra Written 4000000 spots for SRR1314159/SRR1314159.sra 2020-06-16T00:33:03 prefetch.2.10.7: 1) Downloading 'SRR1314160'... 2020-06-16T00:33:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:33:50 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:33:50 prefetch.2.10.7: 'SRR1314160' is valid 2020-06-16T00:33:50 prefetch.2.10.7: 1) 'SRR1314160' was downloaded successfully 2020-06-16T00:33:50 prefetch.2.10.7: 'SRR1314160' has 0 unresolved dependencies Read 4000000 spots for SRR1314160/SRR1314160.sra Written 4000000 spots for SRR1314160/SRR1314160.sra 2020-06-16T00:34:16 prefetch.2.10.7: 1) Downloading 'SRR1314161'... 2020-06-16T00:34:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:34:38 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:34:38 prefetch.2.10.7: 'SRR1314161' is valid 2020-06-16T00:34:38 prefetch.2.10.7: 1) 'SRR1314161' was downloaded successfully 2020-06-16T00:34:38 prefetch.2.10.7: 'SRR1314161' has 0 unresolved dependencies Read 772844 spots for SRR1314161/SRR1314161.sra Written 772844 spots for SRR1314161/SRR1314161.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: 00:01:56 8772844 reads; of these: 8772844 (100.00%) were unpaired; of these: 4558264 (51.96%) aligned 0 times 3587193 (40.89%) aligned exactly 1 time 627387 (7.15%) aligned >1 times 48.04% overall alignment rate Time searching: 00:01:57 Overall time: 00:01:57 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] 4184310 / 4214580 = 0.9928 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 09:37:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.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 09:37:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:37:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:37:54: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:37:54: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:37:54: #1 total tags in treatment: 30270 INFO @ Tue, 16 Jun 2020 09:37:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:37:54: #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 09:37:54: #1 tags after filtering in treatment: 30270 INFO @ Tue, 16 Jun 2020 09:37:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:37:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:37:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:37:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:37:54: #2 number of paired peaks: 3789 INFO @ Tue, 16 Jun 2020 09:37:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:37:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:37:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:37:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:37:54: #2 predicted fragment length is 103 bps INFO @ Tue, 16 Jun 2020 09:37:54: #2 alternative fragment length(s) may be 6,103,160,209,273,313,343,380,417,495,542,564 bps INFO @ Tue, 16 Jun 2020 09:37:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.05_model.r WARNING @ Tue, 16 Jun 2020 09:37:54: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:37:54: #2 You may need to consider one of the other alternative d(s): 6,103,160,209,273,313,343,380,417,495,542,564 WARNING @ Tue, 16 Jun 2020 09:37:54: #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 09:37:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:37:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:37:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:37:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:37:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:37:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.05_summits.bed INFO @ Tue, 16 Jun 2020 09:37:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (57 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 09:38:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.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 09:38:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:24: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:38:24: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:38:24: #1 total tags in treatment: 30270 INFO @ Tue, 16 Jun 2020 09:38:24: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:38:24: #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 09:38:24: #1 tags after filtering in treatment: 30270 INFO @ Tue, 16 Jun 2020 09:38:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:38:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:38:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:38:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:38:24: #2 number of paired peaks: 3789 INFO @ Tue, 16 Jun 2020 09:38:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:38:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:38:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:38:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:38:24: #2 predicted fragment length is 103 bps INFO @ Tue, 16 Jun 2020 09:38:24: #2 alternative fragment length(s) may be 6,103,160,209,273,313,343,380,417,495,542,564 bps INFO @ Tue, 16 Jun 2020 09:38:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.10_model.r WARNING @ Tue, 16 Jun 2020 09:38:24: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:38:24: #2 You may need to consider one of the other alternative d(s): 6,103,160,209,273,313,343,380,417,495,542,564 WARNING @ Tue, 16 Jun 2020 09:38:24: #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 09:38:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:38:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:38:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:38:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:38:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:38:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.10_summits.bed INFO @ Tue, 16 Jun 2020 09:38:24: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (22 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 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 09:38:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.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 09:38:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:38:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:38:54: #1 tag size is determined as 76 bps INFO @ Tue, 16 Jun 2020 09:38:54: #1 tag size = 76 INFO @ Tue, 16 Jun 2020 09:38:54: #1 total tags in treatment: 30270 INFO @ Tue, 16 Jun 2020 09:38:54: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:38:54: #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 09:38:54: #1 tags after filtering in treatment: 30270 INFO @ Tue, 16 Jun 2020 09:38:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:38:54: #1 finished! INFO @ Tue, 16 Jun 2020 09:38:54: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:38:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:38:54: #2 number of paired peaks: 3789 INFO @ Tue, 16 Jun 2020 09:38:54: start model_add_line... INFO @ Tue, 16 Jun 2020 09:38:54: start X-correlation... INFO @ Tue, 16 Jun 2020 09:38:54: end of X-cor INFO @ Tue, 16 Jun 2020 09:38:54: #2 finished! INFO @ Tue, 16 Jun 2020 09:38:54: #2 predicted fragment length is 103 bps INFO @ Tue, 16 Jun 2020 09:38:54: #2 alternative fragment length(s) may be 6,103,160,209,273,313,343,380,417,495,542,564 bps INFO @ Tue, 16 Jun 2020 09:38:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.20_model.r WARNING @ Tue, 16 Jun 2020 09:38:54: #2 Since the d (103) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:38:54: #2 You may need to consider one of the other alternative d(s): 6,103,160,209,273,313,343,380,417,495,542,564 WARNING @ Tue, 16 Jun 2020 09:38:54: #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 09:38:54: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:38:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:38:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:38:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:38:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:38:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX560682/SRX560682.20_summits.bed INFO @ Tue, 16 Jun 2020 09:38:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (14 records, 4 fields): 1 millis CompletedMACS2peakCalling