Job ID = 6366707 SRX = SRX2228862 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:01:54 prefetch.2.10.7: 1) Downloading 'SRR4380318'... 2020-06-15T23:01:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:03:42 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:03:42 prefetch.2.10.7: 1) 'SRR4380318' was downloaded successfully Read 30487356 spots for SRR4380318/SRR4380318.sra Written 30487356 spots for SRR4380318/SRR4380318.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: 00:04:34 30487356 reads; of these: 30487356 (100.00%) were unpaired; of these: 2944486 (9.66%) aligned 0 times 22653323 (74.30%) aligned exactly 1 time 4889547 (16.04%) aligned >1 times 90.34% overall alignment rate Time searching: 00:04:34 Overall time: 00:04:34 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] 22065378 / 27542870 = 0.8011 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 08:13:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.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 08:13:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:38: 1000000 INFO @ Tue, 16 Jun 2020 08:13:43: 2000000 INFO @ Tue, 16 Jun 2020 08:13:48: 3000000 INFO @ Tue, 16 Jun 2020 08:13:53: 4000000 INFO @ Tue, 16 Jun 2020 08:13:58: 5000000 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 08:14:01: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:14:01: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:14:01: #1 total tags in treatment: 5477492 INFO @ Tue, 16 Jun 2020 08:14:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:01: #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 08:14:01: #1 tags after filtering in treatment: 5477492 INFO @ Tue, 16 Jun 2020 08:14:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:01: #2 number of paired peaks: 1310 INFO @ Tue, 16 Jun 2020 08:14:01: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:01: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:01: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:01: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:01: #2 predicted fragment length is 114 bps INFO @ Tue, 16 Jun 2020 08:14:01: #2 alternative fragment length(s) may be 4,114 bps INFO @ Tue, 16 Jun 2020 08:14:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.05_model.r INFO @ Tue, 16 Jun 2020 08:14:01: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.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 08:14:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:08: 1000000 INFO @ Tue, 16 Jun 2020 08:14:13: 2000000 INFO @ Tue, 16 Jun 2020 08:14:15: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:18: 3000000 INFO @ Tue, 16 Jun 2020 08:14:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.05_summits.bed INFO @ Tue, 16 Jun 2020 08:14:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2032 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:14:23: 4000000 INFO @ Tue, 16 Jun 2020 08:14:28: 5000000 INFO @ Tue, 16 Jun 2020 08:14:30: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:14:30: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:14:30: #1 total tags in treatment: 5477492 INFO @ Tue, 16 Jun 2020 08:14:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:30: #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 08:14:30: #1 tags after filtering in treatment: 5477492 INFO @ Tue, 16 Jun 2020 08:14:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:30: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:30: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:30: #2 looking for paired plus/minus strand peaks... 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 08:14:31: #2 number of paired peaks: 1310 INFO @ Tue, 16 Jun 2020 08:14:31: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:31: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:31: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:31: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:31: #2 predicted fragment length is 114 bps INFO @ Tue, 16 Jun 2020 08:14:31: #2 alternative fragment length(s) may be 4,114 bps INFO @ Tue, 16 Jun 2020 08:14:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.10_model.r INFO @ Tue, 16 Jun 2020 08:14:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.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 08:14:35: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:35: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:40: 1000000 INFO @ Tue, 16 Jun 2020 08:14:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:44: 2000000 INFO @ Tue, 16 Jun 2020 08:14:49: 3000000 INFO @ Tue, 16 Jun 2020 08:14:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.10_summits.bed INFO @ Tue, 16 Jun 2020 08:14:50: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1097 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:14:54: 4000000 INFO @ Tue, 16 Jun 2020 08:14:59: 5000000 INFO @ Tue, 16 Jun 2020 08:15:01: #1 tag size is determined as 35 bps INFO @ Tue, 16 Jun 2020 08:15:01: #1 tag size = 35 INFO @ Tue, 16 Jun 2020 08:15:01: #1 total tags in treatment: 5477492 INFO @ Tue, 16 Jun 2020 08:15:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:15:01: #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 08:15:01: #1 tags after filtering in treatment: 5477492 INFO @ Tue, 16 Jun 2020 08:15:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:15:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:15:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:15:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:15:02: #2 number of paired peaks: 1310 INFO @ Tue, 16 Jun 2020 08:15:02: start model_add_line... INFO @ Tue, 16 Jun 2020 08:15:02: start X-correlation... INFO @ Tue, 16 Jun 2020 08:15:02: end of X-cor INFO @ Tue, 16 Jun 2020 08:15:02: #2 finished! INFO @ Tue, 16 Jun 2020 08:15:02: #2 predicted fragment length is 114 bps INFO @ Tue, 16 Jun 2020 08:15:02: #2 alternative fragment length(s) may be 4,114 bps INFO @ Tue, 16 Jun 2020 08:15:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.20_model.r INFO @ Tue, 16 Jun 2020 08:15:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:15:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:15:14: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:15:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:15:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:15:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228862/SRX2228862.20_summits.bed INFO @ Tue, 16 Jun 2020 08:15:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (598 records, 4 fields): 1 millis CompletedMACS2peakCalling