Job ID = 6509171 SRX = SRX706812 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T15:18:14 prefetch.2.10.7: 1) Downloading 'SRR1581493'... 2020-06-26T15:18:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T15:19:43 prefetch.2.10.7: HTTPS download succeed 2020-06-26T15:19:44 prefetch.2.10.7: 'SRR1581493' is valid 2020-06-26T15:19:44 prefetch.2.10.7: 1) 'SRR1581493' was downloaded successfully Read 17095851 spots for SRR1581493/SRR1581493.sra Written 17095851 spots for SRR1581493/SRR1581493.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: 00:02:15 17095851 reads; of these: 17095851 (100.00%) were unpaired; of these: 10247952 (59.94%) aligned 0 times 5572898 (32.60%) aligned exactly 1 time 1275001 (7.46%) aligned >1 times 40.06% overall alignment rate Time searching: 00:02:15 Overall time: 00:02:15 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] 3151416 / 6847899 = 0.4602 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 @ Sat, 27 Jun 2020 00:24:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.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 @ Sat, 27 Jun 2020 00:24:44: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:24:44: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:24:51: 1000000 INFO @ Sat, 27 Jun 2020 00:24:57: 2000000 INFO @ Sat, 27 Jun 2020 00:25:03: 3000000 INFO @ Sat, 27 Jun 2020 00:25:07: #1 tag size is determined as 44 bps INFO @ Sat, 27 Jun 2020 00:25:07: #1 tag size = 44 INFO @ Sat, 27 Jun 2020 00:25:07: #1 total tags in treatment: 3696483 INFO @ Sat, 27 Jun 2020 00:25:07: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:25:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:25:08: #1 tags after filtering in treatment: 3696388 INFO @ Sat, 27 Jun 2020 00:25:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:25:08: #1 finished! INFO @ Sat, 27 Jun 2020 00:25:08: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:25:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:25:08: #2 number of paired peaks: 605 WARNING @ Sat, 27 Jun 2020 00:25:08: Fewer paired peaks (605) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 605 pairs to build model! INFO @ Sat, 27 Jun 2020 00:25:08: start model_add_line... INFO @ Sat, 27 Jun 2020 00:25:08: start X-correlation... INFO @ Sat, 27 Jun 2020 00:25:08: end of X-cor INFO @ Sat, 27 Jun 2020 00:25:08: #2 finished! INFO @ Sat, 27 Jun 2020 00:25:08: #2 predicted fragment length is 46 bps INFO @ Sat, 27 Jun 2020 00:25:08: #2 alternative fragment length(s) may be 4,46,573 bps INFO @ Sat, 27 Jun 2020 00:25:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.05_model.r WARNING @ Sat, 27 Jun 2020 00:25:08: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:25:08: #2 You may need to consider one of the other alternative d(s): 4,46,573 WARNING @ Sat, 27 Jun 2020 00:25:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:25:08: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:25:08: #3 Pre-compute pvalue-qvalue table... 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 @ Sat, 27 Jun 2020 00:25:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.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 @ Sat, 27 Jun 2020 00:25:14: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:25:14: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:25:17: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:25:21: 1000000 INFO @ Sat, 27 Jun 2020 00:25:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.05_peaks.xls INFO @ Sat, 27 Jun 2020 00:25:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.05_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:25:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.05_summits.bed INFO @ Sat, 27 Jun 2020 00:25:22: Done! pass1 - making usageList (182 chroms): 1 millis pass2 - checking and writing primary data (493 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:25:28: 2000000 INFO @ Sat, 27 Jun 2020 00:25:36: 3000000 INFO @ Sat, 27 Jun 2020 00:25:41: #1 tag size is determined as 44 bps INFO @ Sat, 27 Jun 2020 00:25:41: #1 tag size = 44 INFO @ Sat, 27 Jun 2020 00:25:41: #1 total tags in treatment: 3696483 INFO @ Sat, 27 Jun 2020 00:25:41: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:25:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:25:41: #1 tags after filtering in treatment: 3696388 INFO @ Sat, 27 Jun 2020 00:25:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:25:41: #1 finished! INFO @ Sat, 27 Jun 2020 00:25:41: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:25:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:25:41: #2 number of paired peaks: 605 WARNING @ Sat, 27 Jun 2020 00:25:41: Fewer paired peaks (605) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 605 pairs to build model! INFO @ Sat, 27 Jun 2020 00:25:41: start model_add_line... INFO @ Sat, 27 Jun 2020 00:25:42: start X-correlation... INFO @ Sat, 27 Jun 2020 00:25:42: end of X-cor INFO @ Sat, 27 Jun 2020 00:25:42: #2 finished! INFO @ Sat, 27 Jun 2020 00:25:42: #2 predicted fragment length is 46 bps INFO @ Sat, 27 Jun 2020 00:25:42: #2 alternative fragment length(s) may be 4,46,573 bps INFO @ Sat, 27 Jun 2020 00:25:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.10_model.r WARNING @ Sat, 27 Jun 2020 00:25:42: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:25:42: #2 You may need to consider one of the other alternative d(s): 4,46,573 WARNING @ Sat, 27 Jun 2020 00:25:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:25:42: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:25:42: #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 @ Sat, 27 Jun 2020 00:25:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.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 @ Sat, 27 Jun 2020 00:25:45: #1 read tag files... INFO @ Sat, 27 Jun 2020 00:25:45: #1 read treatment tags... INFO @ Sat, 27 Jun 2020 00:25:50: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:25:51: 1000000 INFO @ Sat, 27 Jun 2020 00:25:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.10_peaks.xls INFO @ Sat, 27 Jun 2020 00:25:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.10_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:25:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.10_summits.bed INFO @ Sat, 27 Jun 2020 00:25:54: Done! pass1 - making usageList (107 chroms): 1 millis pass2 - checking and writing primary data (319 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 27 Jun 2020 00:25:57: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 27 Jun 2020 00:26:04: 3000000 INFO @ Sat, 27 Jun 2020 00:26:08: #1 tag size is determined as 44 bps INFO @ Sat, 27 Jun 2020 00:26:08: #1 tag size = 44 INFO @ Sat, 27 Jun 2020 00:26:08: #1 total tags in treatment: 3696483 INFO @ Sat, 27 Jun 2020 00:26:08: #1 user defined the maximum tags... INFO @ Sat, 27 Jun 2020 00:26:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 27 Jun 2020 00:26:08: #1 tags after filtering in treatment: 3696388 INFO @ Sat, 27 Jun 2020 00:26:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 27 Jun 2020 00:26:08: #1 finished! INFO @ Sat, 27 Jun 2020 00:26:08: #2 Build Peak Model... INFO @ Sat, 27 Jun 2020 00:26:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 27 Jun 2020 00:26:09: #2 number of paired peaks: 605 WARNING @ Sat, 27 Jun 2020 00:26:09: Fewer paired peaks (605) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 605 pairs to build model! INFO @ Sat, 27 Jun 2020 00:26:09: start model_add_line... INFO @ Sat, 27 Jun 2020 00:26:09: start X-correlation... INFO @ Sat, 27 Jun 2020 00:26:09: end of X-cor INFO @ Sat, 27 Jun 2020 00:26:09: #2 finished! INFO @ Sat, 27 Jun 2020 00:26:09: #2 predicted fragment length is 46 bps INFO @ Sat, 27 Jun 2020 00:26:09: #2 alternative fragment length(s) may be 4,46,573 bps INFO @ Sat, 27 Jun 2020 00:26:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.20_model.r WARNING @ Sat, 27 Jun 2020 00:26:09: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 27 Jun 2020 00:26:09: #2 You may need to consider one of the other alternative d(s): 4,46,573 WARNING @ Sat, 27 Jun 2020 00:26:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 27 Jun 2020 00:26:09: #3 Call peaks... INFO @ Sat, 27 Jun 2020 00:26:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 27 Jun 2020 00:26:18: #3 Call peaks for each chromosome... INFO @ Sat, 27 Jun 2020 00:26:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.20_peaks.xls INFO @ Sat, 27 Jun 2020 00:26:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.20_peaks.narrowPeak INFO @ Sat, 27 Jun 2020 00:26:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX706812/SRX706812.20_summits.bed INFO @ Sat, 27 Jun 2020 00:26:22: Done! pass1 - making usageList (86 chroms): 1 millis pass2 - checking and writing primary data (218 records, 4 fields): 4 millis CompletedMACS2peakCalling