Job ID = 6366725 SRX = SRX2228878 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:06:08 prefetch.2.10.7: 1) Downloading 'SRR4380334'... 2020-06-15T23:06:08 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:07:17 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:07:18 prefetch.2.10.7: 'SRR4380334' is valid 2020-06-15T23:07:18 prefetch.2.10.7: 1) 'SRR4380334' was downloaded successfully 2020-06-15T23:07:18 prefetch.2.10.7: 'SRR4380334' has 0 unresolved dependencies Read 19257180 spots for SRR4380334/SRR4380334.sra Written 19257180 spots for SRR4380334/SRR4380334.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: 00:02:37 19257180 reads; of these: 19257180 (100.00%) were unpaired; of these: 13224306 (68.67%) aligned 0 times 5017112 (26.05%) aligned exactly 1 time 1015762 (5.27%) aligned >1 times 31.33% overall alignment rate Time searching: 00:02:37 Overall time: 00:02:37 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] 884130 / 6032874 = 0.1466 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 08:13:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.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 08:13:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:12: 1000000 INFO @ Tue, 16 Jun 2020 08:13:19: 2000000 INFO @ Tue, 16 Jun 2020 08:13:25: 3000000 INFO @ Tue, 16 Jun 2020 08:13:31: 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 08:13:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.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 08:13:36: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:13:36: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:13:37: 5000000 INFO @ Tue, 16 Jun 2020 08:13:38: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:13:38: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:13:38: #1 total tags in treatment: 5148744 INFO @ Tue, 16 Jun 2020 08:13:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:13:38: #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 08:13:38: #1 tags after filtering in treatment: 5148744 INFO @ Tue, 16 Jun 2020 08:13:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:13:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:13:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:13:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:13:38: #2 number of paired peaks: 652 WARNING @ Tue, 16 Jun 2020 08:13:38: Fewer paired peaks (652) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 652 pairs to build model! INFO @ Tue, 16 Jun 2020 08:13:38: start model_add_line... INFO @ Tue, 16 Jun 2020 08:13:38: start X-correlation... INFO @ Tue, 16 Jun 2020 08:13:38: end of X-cor INFO @ Tue, 16 Jun 2020 08:13:38: #2 finished! INFO @ Tue, 16 Jun 2020 08:13:38: #2 predicted fragment length is 117 bps INFO @ Tue, 16 Jun 2020 08:13:38: #2 alternative fragment length(s) may be 117 bps INFO @ Tue, 16 Jun 2020 08:13:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.05_model.r INFO @ Tue, 16 Jun 2020 08:13:38: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:13:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:13:43: 1000000 INFO @ Tue, 16 Jun 2020 08:13:49: 2000000 INFO @ Tue, 16 Jun 2020 08:13:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:13:55: 3000000 INFO @ Tue, 16 Jun 2020 08:13:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:13:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:13:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.05_summits.bed INFO @ Tue, 16 Jun 2020 08:13:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1468 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:14:01: 4000000 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 08:14:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.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 08:14:06: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:14:06: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:14:07: 5000000 INFO @ Tue, 16 Jun 2020 08:14:08: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:14:08: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:14:08: #1 total tags in treatment: 5148744 INFO @ Tue, 16 Jun 2020 08:14:08: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:08: #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 08:14:08: #1 tags after filtering in treatment: 5148744 INFO @ Tue, 16 Jun 2020 08:14:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:08: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:08: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:08: #2 number of paired peaks: 652 WARNING @ Tue, 16 Jun 2020 08:14:08: Fewer paired peaks (652) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 652 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:08: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:09: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:09: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:09: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:09: #2 predicted fragment length is 117 bps INFO @ Tue, 16 Jun 2020 08:14:09: #2 alternative fragment length(s) may be 117 bps INFO @ Tue, 16 Jun 2020 08:14:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.10_model.r INFO @ Tue, 16 Jun 2020 08:14:09: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:14:13: 1000000 INFO @ Tue, 16 Jun 2020 08:14:19: 2000000 INFO @ Tue, 16 Jun 2020 08:14:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:25: 3000000 INFO @ Tue, 16 Jun 2020 08:14:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.10_summits.bed INFO @ Tue, 16 Jun 2020 08:14:28: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (918 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:14:31: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:14:37: 5000000 INFO @ Tue, 16 Jun 2020 08:14:38: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:14:38: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:14:38: #1 total tags in treatment: 5148744 INFO @ Tue, 16 Jun 2020 08:14:38: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:14:38: #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 08:14:38: #1 tags after filtering in treatment: 5148744 INFO @ Tue, 16 Jun 2020 08:14:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:14:38: #1 finished! INFO @ Tue, 16 Jun 2020 08:14:38: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:14:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:14:39: #2 number of paired peaks: 652 WARNING @ Tue, 16 Jun 2020 08:14:39: Fewer paired peaks (652) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 652 pairs to build model! INFO @ Tue, 16 Jun 2020 08:14:39: start model_add_line... INFO @ Tue, 16 Jun 2020 08:14:39: start X-correlation... INFO @ Tue, 16 Jun 2020 08:14:39: end of X-cor INFO @ Tue, 16 Jun 2020 08:14:39: #2 finished! INFO @ Tue, 16 Jun 2020 08:14:39: #2 predicted fragment length is 117 bps INFO @ Tue, 16 Jun 2020 08:14:39: #2 alternative fragment length(s) may be 117 bps INFO @ Tue, 16 Jun 2020 08:14:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.20_model.r INFO @ Tue, 16 Jun 2020 08:14:39: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:14:39: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:14:51: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:14:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:14:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:14:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2228878/SRX2228878.20_summits.bed INFO @ Tue, 16 Jun 2020 08:14:57: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (496 records, 4 fields): 2 millis CompletedMACS2peakCalling