Job ID = 6368094 SRX = SRX466557 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:51:33 prefetch.2.10.7: 1) Downloading 'SRR1163623'... 2020-06-15T23:51:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:53:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:53:24 prefetch.2.10.7: 'SRR1163623' is valid 2020-06-15T23:53:24 prefetch.2.10.7: 1) 'SRR1163623' was downloaded successfully Read 10739261 spots for SRR1163623/SRR1163623.sra Written 10739261 spots for SRR1163623/SRR1163623.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: 00:01:54 10739261 reads; of these: 10739261 (100.00%) were unpaired; of these: 563809 (5.25%) aligned 0 times 9035941 (84.14%) aligned exactly 1 time 1139511 (10.61%) aligned >1 times 94.75% overall alignment rate Time searching: 00:01:54 Overall time: 00:01:54 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] 2117396 / 10175452 = 0.2081 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 08:58:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.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 08:58:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:58:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:02: 1000000 INFO @ Tue, 16 Jun 2020 08:59:06: 2000000 INFO @ Tue, 16 Jun 2020 08:59:11: 3000000 INFO @ Tue, 16 Jun 2020 08:59:15: 4000000 INFO @ Tue, 16 Jun 2020 08:59:19: 5000000 INFO @ Tue, 16 Jun 2020 08:59:24: 6000000 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 08:59:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.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 08:59:27: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:27: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:28: 7000000 INFO @ Tue, 16 Jun 2020 08:59:32: 1000000 INFO @ Tue, 16 Jun 2020 08:59:33: 8000000 INFO @ Tue, 16 Jun 2020 08:59:33: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 08:59:33: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 08:59:33: #1 total tags in treatment: 8058056 INFO @ Tue, 16 Jun 2020 08:59:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:59:33: #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 08:59:33: #1 tags after filtering in treatment: 8058056 INFO @ Tue, 16 Jun 2020 08:59:33: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:59:33: #1 finished! INFO @ Tue, 16 Jun 2020 08:59:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:59:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:59:34: #2 number of paired peaks: 3508 INFO @ Tue, 16 Jun 2020 08:59:34: start model_add_line... INFO @ Tue, 16 Jun 2020 08:59:34: start X-correlation... INFO @ Tue, 16 Jun 2020 08:59:34: end of X-cor INFO @ Tue, 16 Jun 2020 08:59:34: #2 finished! INFO @ Tue, 16 Jun 2020 08:59:34: #2 predicted fragment length is 192 bps INFO @ Tue, 16 Jun 2020 08:59:34: #2 alternative fragment length(s) may be 4,192 bps INFO @ Tue, 16 Jun 2020 08:59:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.05_model.r INFO @ Tue, 16 Jun 2020 08:59:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:59:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:59:36: 2000000 INFO @ Tue, 16 Jun 2020 08:59:40: 3000000 INFO @ Tue, 16 Jun 2020 08:59:45: 4000000 INFO @ Tue, 16 Jun 2020 08:59:49: 5000000 INFO @ Tue, 16 Jun 2020 08:59:54: 6000000 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 08:59:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.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 08:59:57: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:59:57: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:59:58: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:59:58: 7000000 INFO @ Tue, 16 Jun 2020 09:00:02: 1000000 INFO @ Tue, 16 Jun 2020 09:00:03: 8000000 INFO @ Tue, 16 Jun 2020 09:00:03: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:00:03: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:00:03: #1 total tags in treatment: 8058056 INFO @ Tue, 16 Jun 2020 09:00:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:00:03: #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 09:00:03: #1 tags after filtering in treatment: 8058056 INFO @ Tue, 16 Jun 2020 09:00:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:00:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:00:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:00:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:00:04: #2 number of paired peaks: 3508 INFO @ Tue, 16 Jun 2020 09:00:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:00:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:00:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:00:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:00:04: #2 predicted fragment length is 192 bps INFO @ Tue, 16 Jun 2020 09:00:04: #2 alternative fragment length(s) may be 4,192 bps INFO @ Tue, 16 Jun 2020 09:00:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.10_model.r INFO @ Tue, 16 Jun 2020 09:00:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:00:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:00:07: 2000000 INFO @ Tue, 16 Jun 2020 09:00:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:00:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:00:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.05_summits.bed INFO @ Tue, 16 Jun 2020 09:00:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4254 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:00:11: 3000000 INFO @ Tue, 16 Jun 2020 09:00:16: 4000000 INFO @ Tue, 16 Jun 2020 09:00:21: 5000000 INFO @ Tue, 16 Jun 2020 09:00:26: 6000000 INFO @ Tue, 16 Jun 2020 09:00:28: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:00:31: 7000000 INFO @ Tue, 16 Jun 2020 09:00:36: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:00:36: #1 tag size is determined as 42 bps INFO @ Tue, 16 Jun 2020 09:00:36: #1 tag size = 42 INFO @ Tue, 16 Jun 2020 09:00:36: #1 total tags in treatment: 8058056 INFO @ Tue, 16 Jun 2020 09:00:36: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:00:36: #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 09:00:37: #1 tags after filtering in treatment: 8058056 INFO @ Tue, 16 Jun 2020 09:00:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:00:37: #1 finished! INFO @ Tue, 16 Jun 2020 09:00:37: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:00:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:00:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:00:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:00:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.10_summits.bed INFO @ Tue, 16 Jun 2020 09:00:37: Done! INFO @ Tue, 16 Jun 2020 09:00:37: #2 number of paired peaks: 3508 INFO @ Tue, 16 Jun 2020 09:00:37: start model_add_line... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2582 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:00:38: start X-correlation... INFO @ Tue, 16 Jun 2020 09:00:38: end of X-cor INFO @ Tue, 16 Jun 2020 09:00:38: #2 finished! INFO @ Tue, 16 Jun 2020 09:00:38: #2 predicted fragment length is 192 bps INFO @ Tue, 16 Jun 2020 09:00:38: #2 alternative fragment length(s) may be 4,192 bps INFO @ Tue, 16 Jun 2020 09:00:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.20_model.r INFO @ Tue, 16 Jun 2020 09:00:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:00:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:01:01: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:01:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:01:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:01:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX466557/SRX466557.20_summits.bed INFO @ Tue, 16 Jun 2020 09:01:10: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1192 records, 4 fields): 4 millis CompletedMACS2peakCalling