Job ID = 6365948 SRX = SRX043880 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:37:36 prefetch.2.10.7: 1) Downloading 'SRR107355'... 2020-06-15T22:37:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:38:29 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:38:30 prefetch.2.10.7: 'SRR107355' is valid 2020-06-15T22:38:30 prefetch.2.10.7: 1) 'SRR107355' was downloaded successfully Read 7075959 spots for SRR107355/SRR107355.sra Written 7075959 spots for SRR107355/SRR107355.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: 00:00:54 7075959 reads; of these: 7075959 (100.00%) were unpaired; of these: 2614814 (36.95%) aligned 0 times 4007696 (56.64%) aligned exactly 1 time 453449 (6.41%) aligned >1 times 63.05% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 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] 1467580 / 4461145 = 0.3290 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 07:41:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.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 07:41:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:41:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:41:22: 1000000 INFO @ Tue, 16 Jun 2020 07:41:27: 2000000 INFO @ Tue, 16 Jun 2020 07:41:32: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:41:32: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:41:32: #1 total tags in treatment: 2993565 INFO @ Tue, 16 Jun 2020 07:41:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:41:32: #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 07:41:32: #1 tags after filtering in treatment: 2993565 INFO @ Tue, 16 Jun 2020 07:41:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:41:32: #1 finished! INFO @ Tue, 16 Jun 2020 07:41:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:41:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:41:33: #2 number of paired peaks: 3207 INFO @ Tue, 16 Jun 2020 07:41:33: start model_add_line... INFO @ Tue, 16 Jun 2020 07:41:33: start X-correlation... INFO @ Tue, 16 Jun 2020 07:41:33: end of X-cor INFO @ Tue, 16 Jun 2020 07:41:33: #2 finished! INFO @ Tue, 16 Jun 2020 07:41:33: #2 predicted fragment length is 127 bps INFO @ Tue, 16 Jun 2020 07:41:33: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 16 Jun 2020 07:41:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.05_model.r INFO @ Tue, 16 Jun 2020 07:41:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:41:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:41:40: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:41:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:41:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:41:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.05_summits.bed INFO @ Tue, 16 Jun 2020 07:41:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2790 records, 4 fields): 6 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 07:41:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.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 07:41:46: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:41:46: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:41:51: 1000000 INFO @ Tue, 16 Jun 2020 07:41:57: 2000000 INFO @ Tue, 16 Jun 2020 07:42:02: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:42:02: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:42:02: #1 total tags in treatment: 2993565 INFO @ Tue, 16 Jun 2020 07:42:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:02: #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 07:42:02: #1 tags after filtering in treatment: 2993565 INFO @ Tue, 16 Jun 2020 07:42:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:02: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:02: #2 number of paired peaks: 3207 INFO @ Tue, 16 Jun 2020 07:42:02: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:03: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:03: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:03: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:03: #2 predicted fragment length is 127 bps INFO @ Tue, 16 Jun 2020 07:42:03: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 16 Jun 2020 07:42:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.10_model.r INFO @ Tue, 16 Jun 2020 07:42:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:42:10: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:42:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:42:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:42:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.10_summits.bed INFO @ Tue, 16 Jun 2020 07:42:13: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1017 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 07:42:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.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 07:42:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:42:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:42:22: 1000000 INFO @ Tue, 16 Jun 2020 07:42:27: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:42:33: #1 tag size is determined as 34 bps INFO @ Tue, 16 Jun 2020 07:42:33: #1 tag size = 34 INFO @ Tue, 16 Jun 2020 07:42:33: #1 total tags in treatment: 2993565 INFO @ Tue, 16 Jun 2020 07:42:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:42:33: #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 07:42:33: #1 tags after filtering in treatment: 2993565 INFO @ Tue, 16 Jun 2020 07:42:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:42:33: #1 finished! INFO @ Tue, 16 Jun 2020 07:42:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:42:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:42:33: #2 number of paired peaks: 3207 INFO @ Tue, 16 Jun 2020 07:42:33: start model_add_line... INFO @ Tue, 16 Jun 2020 07:42:33: start X-correlation... INFO @ Tue, 16 Jun 2020 07:42:33: end of X-cor INFO @ Tue, 16 Jun 2020 07:42:33: #2 finished! INFO @ Tue, 16 Jun 2020 07:42:33: #2 predicted fragment length is 127 bps INFO @ Tue, 16 Jun 2020 07:42:33: #2 alternative fragment length(s) may be 127 bps INFO @ Tue, 16 Jun 2020 07:42:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.20_model.r INFO @ Tue, 16 Jun 2020 07:42:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:42:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:42:41: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:42:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:42:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:42:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX043880/SRX043880.20_summits.bed INFO @ Tue, 16 Jun 2020 07:42:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (276 records, 4 fields): 1 millis CompletedMACS2peakCalling