Job ID = 6452652 SRX = SRX025463 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:41:07 prefetch.2.10.7: 1) Downloading 'SRR063856'... 2020-06-21T07:41:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:44:04 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:44:04 prefetch.2.10.7: 'SRR063856' is valid 2020-06-21T07:44:04 prefetch.2.10.7: 1) 'SRR063856' was downloaded successfully Read 9053691 spots for SRR063856/SRR063856.sra Written 9053691 spots for SRR063856/SRR063856.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: 00:01:50 9053691 reads; of these: 9053691 (100.00%) were unpaired; of these: 347256 (3.84%) aligned 0 times 6884810 (76.04%) aligned exactly 1 time 1821625 (20.12%) aligned >1 times 96.16% overall alignment rate Time searching: 00:01:50 Overall time: 00:01:50 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 785709 / 8706435 = 0.0902 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 @ Sun, 21 Jun 2020 16:48:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 16:48:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:48:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:48:54: 1000000 INFO @ Sun, 21 Jun 2020 16:49:00: 2000000 INFO @ Sun, 21 Jun 2020 16:49:05: 3000000 INFO @ Sun, 21 Jun 2020 16:49:10: 4000000 INFO @ Sun, 21 Jun 2020 16:49:15: 5000000 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 @ Sun, 21 Jun 2020 16:49:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 16:49:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:49:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:49:21: 6000000 INFO @ Sun, 21 Jun 2020 16:49:25: 1000000 INFO @ Sun, 21 Jun 2020 16:49:26: 7000000 INFO @ Sun, 21 Jun 2020 16:49:30: 2000000 INFO @ Sun, 21 Jun 2020 16:49:32: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:49:32: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:49:32: #1 total tags in treatment: 7920726 INFO @ Sun, 21 Jun 2020 16:49:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:49:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 16:49:32: #1 tags after filtering in treatment: 7920687 INFO @ Sun, 21 Jun 2020 16:49:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:49:32: #1 finished! INFO @ Sun, 21 Jun 2020 16:49:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:49:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:49:33: #2 number of paired peaks: 281 WARNING @ Sun, 21 Jun 2020 16:49:33: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Sun, 21 Jun 2020 16:49:33: start model_add_line... INFO @ Sun, 21 Jun 2020 16:49:33: start X-correlation... INFO @ Sun, 21 Jun 2020 16:49:33: end of X-cor INFO @ Sun, 21 Jun 2020 16:49:33: #2 finished! INFO @ Sun, 21 Jun 2020 16:49:33: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 16:49:33: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 21 Jun 2020 16:49:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.05_model.r INFO @ Sun, 21 Jun 2020 16:49:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:49:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:49:35: 3000000 INFO @ Sun, 21 Jun 2020 16:49:41: 4000000 INFO @ Sun, 21 Jun 2020 16:49:46: 5000000 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 @ Sun, 21 Jun 2020 16:49:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Sun, 21 Jun 2020 16:49:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:49:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:49:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:49:51: 6000000 INFO @ Sun, 21 Jun 2020 16:49:55: 1000000 INFO @ Sun, 21 Jun 2020 16:49:57: 7000000 INFO @ Sun, 21 Jun 2020 16:49:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:49:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:49:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.05_summits.bed INFO @ Sun, 21 Jun 2020 16:49:58: Done! pass1 - making usageList (241 chroms): 1 millis pass2 - checking and writing primary data (687 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:50:00: 2000000 INFO @ Sun, 21 Jun 2020 16:50:02: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:50:02: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:50:02: #1 total tags in treatment: 7920726 INFO @ Sun, 21 Jun 2020 16:50:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:50:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 16:50:02: #1 tags after filtering in treatment: 7920687 INFO @ Sun, 21 Jun 2020 16:50:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:50:02: #1 finished! INFO @ Sun, 21 Jun 2020 16:50:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:50:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:50:03: #2 number of paired peaks: 281 WARNING @ Sun, 21 Jun 2020 16:50:03: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Sun, 21 Jun 2020 16:50:03: start model_add_line... INFO @ Sun, 21 Jun 2020 16:50:03: start X-correlation... INFO @ Sun, 21 Jun 2020 16:50:03: end of X-cor INFO @ Sun, 21 Jun 2020 16:50:03: #2 finished! INFO @ Sun, 21 Jun 2020 16:50:03: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 16:50:03: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 21 Jun 2020 16:50:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.10_model.r INFO @ Sun, 21 Jun 2020 16:50:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:50:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:50:05: 3000000 INFO @ Sun, 21 Jun 2020 16:50:11: 4000000 INFO @ Sun, 21 Jun 2020 16:50:16: 5000000 INFO @ Sun, 21 Jun 2020 16:50:20: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:50:21: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:50:26: 7000000 INFO @ Sun, 21 Jun 2020 16:50:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:50:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:50:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.10_summits.bed INFO @ Sun, 21 Jun 2020 16:50:29: Done! pass1 - making usageList (173 chroms): 1 millis pass2 - checking and writing primary data (361 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:50:31: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:50:31: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:50:31: #1 total tags in treatment: 7920726 INFO @ Sun, 21 Jun 2020 16:50:31: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:50:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 16:50:32: #1 tags after filtering in treatment: 7920687 INFO @ Sun, 21 Jun 2020 16:50:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:50:32: #1 finished! INFO @ Sun, 21 Jun 2020 16:50:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:50:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:50:32: #2 number of paired peaks: 281 WARNING @ Sun, 21 Jun 2020 16:50:32: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Sun, 21 Jun 2020 16:50:32: start model_add_line... INFO @ Sun, 21 Jun 2020 16:50:32: start X-correlation... INFO @ Sun, 21 Jun 2020 16:50:32: end of X-cor INFO @ Sun, 21 Jun 2020 16:50:32: #2 finished! INFO @ Sun, 21 Jun 2020 16:50:32: #2 predicted fragment length is 148 bps INFO @ Sun, 21 Jun 2020 16:50:32: #2 alternative fragment length(s) may be 148 bps INFO @ Sun, 21 Jun 2020 16:50:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.20_model.r INFO @ Sun, 21 Jun 2020 16:50:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:50:32: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:50:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:50:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:50:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:50:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX025463/SRX025463.20_summits.bed INFO @ Sun, 21 Jun 2020 16:50:57: Done! pass1 - making usageList (90 chroms): 1 millis pass2 - checking and writing primary data (173 records, 4 fields): 4 millis CompletedMACS2peakCalling