Job ID = 6366089 SRX = SRX059267 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:40:06 prefetch.2.10.7: 1) Downloading 'SRR190707'... 2020-06-15T22:40:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:41:17 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:41:17 prefetch.2.10.7: 'SRR190707' is valid 2020-06-15T22:41:17 prefetch.2.10.7: 1) 'SRR190707' was downloaded successfully Read 8845185 spots for SRR190707/SRR190707.sra Written 8845185 spots for SRR190707/SRR190707.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: 00:00:29 8845185 reads; of these: 8845185 (100.00%) were unpaired; of these: 7706869 (87.13%) aligned 0 times 925794 (10.47%) aligned exactly 1 time 212522 (2.40%) aligned >1 times 12.87% overall alignment rate Time searching: 00:00:29 Overall time: 00:00:29 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] 172345 / 1138316 = 0.1514 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 07:43:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.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 07:43:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:09: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:43:09: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:43:09: #1 total tags in treatment: 965971 INFO @ Tue, 16 Jun 2020 07:43:09: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:09: #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 07:43:09: #1 tags after filtering in treatment: 965971 INFO @ Tue, 16 Jun 2020 07:43:09: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:09: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:09: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:09: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:09: #2 number of paired peaks: 1204 INFO @ Tue, 16 Jun 2020 07:43:09: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:09: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:09: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:09: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:09: #2 predicted fragment length is 167 bps INFO @ Tue, 16 Jun 2020 07:43:09: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 16 Jun 2020 07:43:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.05_model.r INFO @ Tue, 16 Jun 2020 07:43:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:43:12: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:43:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.05_peaks.xls INFO @ Tue, 16 Jun 2020 07:43:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:43:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.05_summits.bed INFO @ Tue, 16 Jun 2020 07:43:13: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (862 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 07:43:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.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 07:43:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 07:43:32: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:43:32: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:43:32: #1 total tags in treatment: 965971 INFO @ Tue, 16 Jun 2020 07:43:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:43:32: #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 07:43:32: #1 tags after filtering in treatment: 965971 INFO @ Tue, 16 Jun 2020 07:43:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:43:32: #1 finished! INFO @ Tue, 16 Jun 2020 07:43:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:43:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 07:43:32: #2 number of paired peaks: 1204 INFO @ Tue, 16 Jun 2020 07:43:32: start model_add_line... INFO @ Tue, 16 Jun 2020 07:43:32: start X-correlation... INFO @ Tue, 16 Jun 2020 07:43:32: end of X-cor INFO @ Tue, 16 Jun 2020 07:43:32: #2 finished! INFO @ Tue, 16 Jun 2020 07:43:32: #2 predicted fragment length is 167 bps INFO @ Tue, 16 Jun 2020 07:43:32: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 16 Jun 2020 07:43:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.10_model.r INFO @ Tue, 16 Jun 2020 07:43:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:43:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:43:35: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:43:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.10_peaks.xls INFO @ Tue, 16 Jun 2020 07:43:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:43:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.10_summits.bed INFO @ Tue, 16 Jun 2020 07:43:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (567 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 07:43:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.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 07:43:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 07:43:57: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 07:44:02: #1 tag size is determined as 28 bps INFO @ Tue, 16 Jun 2020 07:44:02: #1 tag size = 28 INFO @ Tue, 16 Jun 2020 07:44:02: #1 total tags in treatment: 965971 INFO @ Tue, 16 Jun 2020 07:44:02: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 07:44:02: #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 07:44:02: #1 tags after filtering in treatment: 965971 INFO @ Tue, 16 Jun 2020 07:44:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 07:44:02: #1 finished! INFO @ Tue, 16 Jun 2020 07:44:02: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 07:44:02: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 07:44:02: #2 number of paired peaks: 1204 INFO @ Tue, 16 Jun 2020 07:44:02: start model_add_line... INFO @ Tue, 16 Jun 2020 07:44:02: start X-correlation... INFO @ Tue, 16 Jun 2020 07:44:02: end of X-cor INFO @ Tue, 16 Jun 2020 07:44:02: #2 finished! INFO @ Tue, 16 Jun 2020 07:44:02: #2 predicted fragment length is 167 bps INFO @ Tue, 16 Jun 2020 07:44:02: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 16 Jun 2020 07:44:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.20_model.r INFO @ Tue, 16 Jun 2020 07:44:02: #3 Call peaks... INFO @ Tue, 16 Jun 2020 07:44:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 07:44:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 07:44:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.20_peaks.xls INFO @ Tue, 16 Jun 2020 07:44:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 07:44:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX059267/SRX059267.20_summits.bed INFO @ Tue, 16 Jun 2020 07:44:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (328 records, 4 fields): 2 millis CompletedMACS2peakCalling