Job ID = 6452558 SRX = SRX016164 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:38:21 prefetch.2.10.7: 1) Downloading 'SRR034730'... 2020-06-21T07:38:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:41:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:41:09 prefetch.2.10.7: 'SRR034730' is valid 2020-06-21T07:41:09 prefetch.2.10.7: 1) 'SRR034730' was downloaded successfully Read 13990339 spots for SRR034730/SRR034730.sra Written 13990339 spots for SRR034730/SRR034730.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: 00:02:28 13990339 reads; of these: 13990339 (100.00%) were unpaired; of these: 1765638 (12.62%) aligned 0 times 9930469 (70.98%) aligned exactly 1 time 2294232 (16.40%) aligned >1 times 87.38% overall alignment rate Time searching: 00:02:28 Overall time: 00:02:28 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] 957020 / 12224701 = 0.0783 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 16:48:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.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 16:48:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:48:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:48:32: 1000000 INFO @ Sun, 21 Jun 2020 16:48:37: 2000000 INFO @ Sun, 21 Jun 2020 16:48:42: 3000000 INFO @ Sun, 21 Jun 2020 16:48:46: 4000000 INFO @ Sun, 21 Jun 2020 16:48:51: 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 16:48:56: 6000000 INFO @ Sun, 21 Jun 2020 16:48:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.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 16:48:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:48:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:49:01: 7000000 INFO @ Sun, 21 Jun 2020 16:49:03: 1000000 INFO @ Sun, 21 Jun 2020 16:49:05: 8000000 INFO @ Sun, 21 Jun 2020 16:49:08: 2000000 INFO @ Sun, 21 Jun 2020 16:49:10: 9000000 INFO @ Sun, 21 Jun 2020 16:49:13: 3000000 INFO @ Sun, 21 Jun 2020 16:49:16: 10000000 INFO @ Sun, 21 Jun 2020 16:49:17: 4000000 INFO @ Sun, 21 Jun 2020 16:49:21: 11000000 INFO @ Sun, 21 Jun 2020 16:49:22: 5000000 INFO @ Sun, 21 Jun 2020 16:49:23: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:49:23: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:49:23: #1 total tags in treatment: 11267681 INFO @ Sun, 21 Jun 2020 16:49:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:49:23: #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 16:49:23: #1 tags after filtering in treatment: 11267657 INFO @ Sun, 21 Jun 2020 16:49:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:49:23: #1 finished! INFO @ Sun, 21 Jun 2020 16:49:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:49:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:49:24: #2 number of paired peaks: 161 WARNING @ Sun, 21 Jun 2020 16:49:24: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sun, 21 Jun 2020 16:49:24: start model_add_line... INFO @ Sun, 21 Jun 2020 16:49:24: start X-correlation... INFO @ Sun, 21 Jun 2020 16:49:24: end of X-cor INFO @ Sun, 21 Jun 2020 16:49:24: #2 finished! INFO @ Sun, 21 Jun 2020 16:49:24: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 16:49:24: #2 alternative fragment length(s) may be 80 bps INFO @ Sun, 21 Jun 2020 16:49:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.05_model.r INFO @ Sun, 21 Jun 2020 16:49:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:49:24: #3 Pre-compute pvalue-qvalue table... 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 16:49:27: 6000000 INFO @ Sun, 21 Jun 2020 16:49:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.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 16:49:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:49:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:49:31: 7000000 INFO @ Sun, 21 Jun 2020 16:49:32: 1000000 INFO @ Sun, 21 Jun 2020 16:49:36: 8000000 INFO @ Sun, 21 Jun 2020 16:49:37: 2000000 INFO @ Sun, 21 Jun 2020 16:49:40: 9000000 INFO @ Sun, 21 Jun 2020 16:49:42: 3000000 INFO @ Sun, 21 Jun 2020 16:49:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:49:46: 10000000 INFO @ Sun, 21 Jun 2020 16:49:46: 4000000 INFO @ Sun, 21 Jun 2020 16:49:50: 11000000 INFO @ Sun, 21 Jun 2020 16:49:51: 5000000 INFO @ Sun, 21 Jun 2020 16:49:52: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:49:52: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:49:52: #1 total tags in treatment: 11267681 INFO @ Sun, 21 Jun 2020 16:49:52: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:49:52: #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 16:49:53: #1 tags after filtering in treatment: 11267657 INFO @ Sun, 21 Jun 2020 16:49:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:49:53: #1 finished! INFO @ Sun, 21 Jun 2020 16:49:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:49:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:49:54: #2 number of paired peaks: 161 WARNING @ Sun, 21 Jun 2020 16:49:54: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sun, 21 Jun 2020 16:49:54: start model_add_line... INFO @ Sun, 21 Jun 2020 16:49:54: start X-correlation... INFO @ Sun, 21 Jun 2020 16:49:54: end of X-cor INFO @ Sun, 21 Jun 2020 16:49:54: #2 finished! INFO @ Sun, 21 Jun 2020 16:49:54: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 16:49:54: #2 alternative fragment length(s) may be 80 bps INFO @ Sun, 21 Jun 2020 16:49:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.10_model.r INFO @ Sun, 21 Jun 2020 16:49:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:49:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:49:55: 6000000 INFO @ Sun, 21 Jun 2020 16:49:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:49:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:49:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.05_summits.bed INFO @ Sun, 21 Jun 2020 16:49:57: Done! pass1 - making usageList (247 chroms): 1 millis pass2 - checking and writing primary data (1387 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:50:00: 7000000 INFO @ Sun, 21 Jun 2020 16:50:04: 8000000 INFO @ Sun, 21 Jun 2020 16:50:09: 9000000 INFO @ Sun, 21 Jun 2020 16:50:14: 10000000 INFO @ Sun, 21 Jun 2020 16:50:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:50:19: 11000000 INFO @ Sun, 21 Jun 2020 16:50:20: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:50:20: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:50:20: #1 total tags in treatment: 11267681 INFO @ Sun, 21 Jun 2020 16:50:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:50:20: #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 16:50:21: #1 tags after filtering in treatment: 11267657 INFO @ Sun, 21 Jun 2020 16:50:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:50:21: #1 finished! INFO @ Sun, 21 Jun 2020 16:50:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:50:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:50:22: #2 number of paired peaks: 161 WARNING @ Sun, 21 Jun 2020 16:50:22: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sun, 21 Jun 2020 16:50:22: start model_add_line... INFO @ Sun, 21 Jun 2020 16:50:22: start X-correlation... INFO @ Sun, 21 Jun 2020 16:50:22: end of X-cor INFO @ Sun, 21 Jun 2020 16:50:22: #2 finished! INFO @ Sun, 21 Jun 2020 16:50:22: #2 predicted fragment length is 80 bps INFO @ Sun, 21 Jun 2020 16:50:22: #2 alternative fragment length(s) may be 80 bps INFO @ Sun, 21 Jun 2020 16:50:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.20_model.r INFO @ Sun, 21 Jun 2020 16:50:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:50:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:50:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:50:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:50:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.10_summits.bed INFO @ Sun, 21 Jun 2020 16:50:26: Done! pass1 - making usageList (164 chroms): 1 millis pass2 - checking and writing primary data (427 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:50:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:50:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:50:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:50:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX016164/SRX016164.20_summits.bed INFO @ Sun, 21 Jun 2020 16:50:54: Done! pass1 - making usageList (77 chroms): 1 millis pass2 - checking and writing primary data (138 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。