Job ID = 6454275 SRX = SRX193632 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:06:54 prefetch.2.10.7: 1) Downloading 'SRR586010'... 2020-06-21T09:06:54 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:11:09 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:11:09 prefetch.2.10.7: 1) 'SRR586010' was downloaded successfully Read 22163454 spots for SRR586010/SRR586010.sra Written 22163454 spots for SRR586010/SRR586010.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: 00:02:55 22163454 reads; of these: 22163454 (100.00%) were unpaired; of these: 17153754 (77.40%) aligned 0 times 3715905 (16.77%) aligned exactly 1 time 1293795 (5.84%) aligned >1 times 22.60% overall alignment rate Time searching: 00:02:55 Overall time: 00:02:55 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] 1330690 / 5009700 = 0.2656 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 18:16:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.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 18:16:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:16:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:16:52: 1000000 INFO @ Sun, 21 Jun 2020 18:16:57: 2000000 INFO @ Sun, 21 Jun 2020 18:17:02: 3000000 INFO @ Sun, 21 Jun 2020 18:17:05: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:17:05: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:17:05: #1 total tags in treatment: 3679010 INFO @ Sun, 21 Jun 2020 18:17:05: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:17:05: #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 18:17:06: #1 tags after filtering in treatment: 3678795 INFO @ Sun, 21 Jun 2020 18:17:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:17:06: #1 finished! INFO @ Sun, 21 Jun 2020 18:17:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:17:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:17:06: #2 number of paired peaks: 817 WARNING @ Sun, 21 Jun 2020 18:17:06: Fewer paired peaks (817) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 817 pairs to build model! INFO @ Sun, 21 Jun 2020 18:17:06: start model_add_line... INFO @ Sun, 21 Jun 2020 18:17:06: start X-correlation... INFO @ Sun, 21 Jun 2020 18:17:06: end of X-cor INFO @ Sun, 21 Jun 2020 18:17:06: #2 finished! INFO @ Sun, 21 Jun 2020 18:17:06: #2 predicted fragment length is 105 bps INFO @ Sun, 21 Jun 2020 18:17:06: #2 alternative fragment length(s) may be 64,105 bps INFO @ Sun, 21 Jun 2020 18:17:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.05_model.r INFO @ Sun, 21 Jun 2020 18:17:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:17:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:17:14: #3 Call peaks for each chromosome... 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 18:17:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.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 18:17:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:17:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:17:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.05_summits.bed INFO @ Sun, 21 Jun 2020 18:17:18: Done! pass1 - making usageList (496 chroms): 1 millis pass2 - checking and writing primary data (1595 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:17:22: 1000000 INFO @ Sun, 21 Jun 2020 18:17:27: 2000000 INFO @ Sun, 21 Jun 2020 18:17:32: 3000000 INFO @ Sun, 21 Jun 2020 18:17:35: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:17:35: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:17:35: #1 total tags in treatment: 3679010 INFO @ Sun, 21 Jun 2020 18:17:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:17:35: #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 18:17:35: #1 tags after filtering in treatment: 3678795 INFO @ Sun, 21 Jun 2020 18:17:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:17:35: #1 finished! INFO @ Sun, 21 Jun 2020 18:17:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:17:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:17:36: #2 number of paired peaks: 817 WARNING @ Sun, 21 Jun 2020 18:17:36: Fewer paired peaks (817) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 817 pairs to build model! INFO @ Sun, 21 Jun 2020 18:17:36: start model_add_line... INFO @ Sun, 21 Jun 2020 18:17:36: start X-correlation... INFO @ Sun, 21 Jun 2020 18:17:36: end of X-cor INFO @ Sun, 21 Jun 2020 18:17:36: #2 finished! INFO @ Sun, 21 Jun 2020 18:17:36: #2 predicted fragment length is 105 bps INFO @ Sun, 21 Jun 2020 18:17:36: #2 alternative fragment length(s) may be 64,105 bps INFO @ Sun, 21 Jun 2020 18:17:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.10_model.r INFO @ Sun, 21 Jun 2020 18:17:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:17:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:17:44: #3 Call peaks for each chromosome... 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 18:17:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.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 18:17:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:17:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:17:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:17:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:17:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.10_summits.bed INFO @ Sun, 21 Jun 2020 18:17:48: Done! pass1 - making usageList (361 chroms): 1 millis pass2 - checking and writing primary data (775 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:17:52: 1000000 INFO @ Sun, 21 Jun 2020 18:17:57: 2000000 INFO @ Sun, 21 Jun 2020 18:18:02: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:18:06: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:18:06: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:18:06: #1 total tags in treatment: 3679010 INFO @ Sun, 21 Jun 2020 18:18:06: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:18:06: #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 18:18:06: #1 tags after filtering in treatment: 3678795 INFO @ Sun, 21 Jun 2020 18:18:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:18:06: #1 finished! INFO @ Sun, 21 Jun 2020 18:18:06: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:18:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:18:06: #2 number of paired peaks: 817 WARNING @ Sun, 21 Jun 2020 18:18:06: Fewer paired peaks (817) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 817 pairs to build model! INFO @ Sun, 21 Jun 2020 18:18:06: start model_add_line... INFO @ Sun, 21 Jun 2020 18:18:06: start X-correlation... INFO @ Sun, 21 Jun 2020 18:18:06: end of X-cor INFO @ Sun, 21 Jun 2020 18:18:06: #2 finished! INFO @ Sun, 21 Jun 2020 18:18:06: #2 predicted fragment length is 105 bps INFO @ Sun, 21 Jun 2020 18:18:06: #2 alternative fragment length(s) may be 64,105 bps INFO @ Sun, 21 Jun 2020 18:18:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.20_model.r INFO @ Sun, 21 Jun 2020 18:18:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:18:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:18:15: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:18:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:18:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:18:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193632/SRX193632.20_summits.bed INFO @ Sun, 21 Jun 2020 18:18:19: Done! pass1 - making usageList (148 chroms): 1 millis pass2 - checking and writing primary data (258 records, 4 fields): 5 millis CompletedMACS2peakCalling