Job ID = 6366606 SRX = SRX208771 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T22:57:38 prefetch.2.10.7: 1) Downloading 'SRR628905'... 2020-06-15T22:57:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T22:59:04 prefetch.2.10.7: HTTPS download succeed 2020-06-15T22:59:04 prefetch.2.10.7: 'SRR628905' is valid 2020-06-15T22:59:04 prefetch.2.10.7: 1) 'SRR628905' was downloaded successfully Read 14095169 spots for SRR628905/SRR628905.sra Written 14095169 spots for SRR628905/SRR628905.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: 00:03:56 14095169 reads; of these: 14095169 (100.00%) were unpaired; of these: 1505040 (10.68%) aligned 0 times 10447401 (74.12%) aligned exactly 1 time 2142728 (15.20%) aligned >1 times 89.32% overall alignment rate Time searching: 00:03:56 Overall time: 00:03:56 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] 6838623 / 12590129 = 0.5432 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 08:07:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.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 08:07:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:15: 1000000 INFO @ Tue, 16 Jun 2020 08:07:21: 2000000 INFO @ Tue, 16 Jun 2020 08:07:27: 3000000 INFO @ Tue, 16 Jun 2020 08:07:33: 4000000 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 08:07:39: 5000000 INFO @ Tue, 16 Jun 2020 08:07:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.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 08:07:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:07:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:07:44: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:07:44: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:07:44: #1 total tags in treatment: 5751506 INFO @ Tue, 16 Jun 2020 08:07:44: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:07:44: #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 08:07:44: #1 tags after filtering in treatment: 5751506 INFO @ Tue, 16 Jun 2020 08:07:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:07:44: #1 finished! INFO @ Tue, 16 Jun 2020 08:07:44: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:07:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:07:45: #2 number of paired peaks: 1082 INFO @ Tue, 16 Jun 2020 08:07:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:07:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:07:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:07:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:07:45: #2 predicted fragment length is 279 bps INFO @ Tue, 16 Jun 2020 08:07:45: #2 alternative fragment length(s) may be 279 bps INFO @ Tue, 16 Jun 2020 08:07:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.05_model.r INFO @ Tue, 16 Jun 2020 08:07:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:07:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:07:46: 1000000 INFO @ Tue, 16 Jun 2020 08:07:52: 2000000 INFO @ Tue, 16 Jun 2020 08:07:58: 3000000 INFO @ Tue, 16 Jun 2020 08:07:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:04: 4000000 INFO @ Tue, 16 Jun 2020 08:08:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.05_summits.bed INFO @ Tue, 16 Jun 2020 08:08:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1356 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 08:08:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.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 08:08:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:08:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:08:11: 5000000 INFO @ Tue, 16 Jun 2020 08:08:16: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:08:16: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:08:16: #1 total tags in treatment: 5751506 INFO @ Tue, 16 Jun 2020 08:08:16: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:16: #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 08:08:16: #1 tags after filtering in treatment: 5751506 INFO @ Tue, 16 Jun 2020 08:08:16: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:16: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:16: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:16: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:17: #2 number of paired peaks: 1082 INFO @ Tue, 16 Jun 2020 08:08:17: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:17: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:17: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:17: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:17: #2 predicted fragment length is 279 bps INFO @ Tue, 16 Jun 2020 08:08:17: #2 alternative fragment length(s) may be 279 bps INFO @ Tue, 16 Jun 2020 08:08:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.10_model.r INFO @ Tue, 16 Jun 2020 08:08:17: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:17: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:08:17: 1000000 INFO @ Tue, 16 Jun 2020 08:08:24: 2000000 INFO @ Tue, 16 Jun 2020 08:08:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:08:32: 3000000 INFO @ Tue, 16 Jun 2020 08:08:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:08:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:08:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.10_summits.bed INFO @ Tue, 16 Jun 2020 08:08:37: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1129 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:08:39: 4000000 INFO @ Tue, 16 Jun 2020 08:08:45: 5000000 INFO @ Tue, 16 Jun 2020 08:08:51: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:08:51: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:08:51: #1 total tags in treatment: 5751506 INFO @ Tue, 16 Jun 2020 08:08:51: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:08:51: #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 08:08:51: #1 tags after filtering in treatment: 5751506 INFO @ Tue, 16 Jun 2020 08:08:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:08:51: #1 finished! INFO @ Tue, 16 Jun 2020 08:08:51: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:08:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:08:51: #2 number of paired peaks: 1082 INFO @ Tue, 16 Jun 2020 08:08:51: start model_add_line... INFO @ Tue, 16 Jun 2020 08:08:51: start X-correlation... INFO @ Tue, 16 Jun 2020 08:08:51: end of X-cor INFO @ Tue, 16 Jun 2020 08:08:51: #2 finished! INFO @ Tue, 16 Jun 2020 08:08:51: #2 predicted fragment length is 279 bps INFO @ Tue, 16 Jun 2020 08:08:51: #2 alternative fragment length(s) may be 279 bps INFO @ Tue, 16 Jun 2020 08:08:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.20_model.r INFO @ Tue, 16 Jun 2020 08:08:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:08:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:09:05: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:09:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:09:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:09:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX208771/SRX208771.20_summits.bed INFO @ Tue, 16 Jun 2020 08:09:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (914 records, 4 fields): 2 millis CompletedMACS2peakCalling