Job ID = 6453733 SRX = SRX1433371 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:24:59 prefetch.2.10.7: 1) Downloading 'SRR2919836'... 2020-06-21T09:24:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:27:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:27:57 prefetch.2.10.7: 1) 'SRR2919836' was downloaded successfully Read 22849299 spots for SRR2919836/SRR2919836.sra Written 22849299 spots for SRR2919836/SRR2919836.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: 00:04:03 22849299 reads; of these: 22849299 (100.00%) were unpaired; of these: 10120686 (44.29%) aligned 0 times 10316206 (45.15%) aligned exactly 1 time 2412407 (10.56%) aligned >1 times 55.71% overall alignment rate Time searching: 00:04:03 Overall time: 00:04:03 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_sort_core] merging from 8 files... [bam_rmdupse_core] 3215734 / 12728613 = 0.2526 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 18:37:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.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 18:37:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:37:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:37:23: 1000000 INFO @ Sun, 21 Jun 2020 18:37:30: 2000000 INFO @ Sun, 21 Jun 2020 18:37:36: 3000000 INFO @ Sun, 21 Jun 2020 18:37:43: 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 @ Sun, 21 Jun 2020 18:37:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.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 18:37:46: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:37:46: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:37:50: 5000000 INFO @ Sun, 21 Jun 2020 18:37:52: 1000000 INFO @ Sun, 21 Jun 2020 18:37:57: 6000000 INFO @ Sun, 21 Jun 2020 18:37:58: 2000000 INFO @ Sun, 21 Jun 2020 18:38:04: 7000000 INFO @ Sun, 21 Jun 2020 18:38:04: 3000000 INFO @ Sun, 21 Jun 2020 18:38:10: 4000000 INFO @ Sun, 21 Jun 2020 18:38:12: 8000000 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 18:38:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.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 18:38:16: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:38:16: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:38:16: 5000000 INFO @ Sun, 21 Jun 2020 18:38:18: 9000000 INFO @ Sun, 21 Jun 2020 18:38:22: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:38:22: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:38:22: #1 total tags in treatment: 9512879 INFO @ Sun, 21 Jun 2020 18:38:22: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:38:22: #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 18:38:23: 1000000 INFO @ Sun, 21 Jun 2020 18:38:23: #1 tags after filtering in treatment: 9512741 INFO @ Sun, 21 Jun 2020 18:38:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:38:23: #1 finished! INFO @ Sun, 21 Jun 2020 18:38:23: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:38:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:38:23: 6000000 INFO @ Sun, 21 Jun 2020 18:38:24: #2 number of paired peaks: 791 WARNING @ Sun, 21 Jun 2020 18:38:24: Fewer paired peaks (791) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 791 pairs to build model! INFO @ Sun, 21 Jun 2020 18:38:24: start model_add_line... INFO @ Sun, 21 Jun 2020 18:38:24: start X-correlation... INFO @ Sun, 21 Jun 2020 18:38:24: end of X-cor INFO @ Sun, 21 Jun 2020 18:38:24: #2 finished! INFO @ Sun, 21 Jun 2020 18:38:24: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 18:38:24: #2 alternative fragment length(s) may be 3,78,96 bps INFO @ Sun, 21 Jun 2020 18:38:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.05_model.r WARNING @ Sun, 21 Jun 2020 18:38:24: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:38:24: #2 You may need to consider one of the other alternative d(s): 3,78,96 WARNING @ Sun, 21 Jun 2020 18:38:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:38:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:38:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:38:29: 2000000 INFO @ Sun, 21 Jun 2020 18:38:30: 7000000 INFO @ Sun, 21 Jun 2020 18:38:35: 3000000 INFO @ Sun, 21 Jun 2020 18:38:37: 8000000 INFO @ Sun, 21 Jun 2020 18:38:42: 4000000 INFO @ Sun, 21 Jun 2020 18:38:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:38:44: 9000000 INFO @ Sun, 21 Jun 2020 18:38:47: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:38:47: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:38:47: #1 total tags in treatment: 9512879 INFO @ Sun, 21 Jun 2020 18:38:47: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:38:47: #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 18:38:48: #1 tags after filtering in treatment: 9512741 INFO @ Sun, 21 Jun 2020 18:38:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:38:48: #1 finished! INFO @ Sun, 21 Jun 2020 18:38:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:38:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:38:48: 5000000 INFO @ Sun, 21 Jun 2020 18:38:49: #2 number of paired peaks: 791 WARNING @ Sun, 21 Jun 2020 18:38:49: Fewer paired peaks (791) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 791 pairs to build model! INFO @ Sun, 21 Jun 2020 18:38:49: start model_add_line... INFO @ Sun, 21 Jun 2020 18:38:49: start X-correlation... INFO @ Sun, 21 Jun 2020 18:38:49: end of X-cor INFO @ Sun, 21 Jun 2020 18:38:49: #2 finished! INFO @ Sun, 21 Jun 2020 18:38:49: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 18:38:49: #2 alternative fragment length(s) may be 3,78,96 bps INFO @ Sun, 21 Jun 2020 18:38:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.10_model.r WARNING @ Sun, 21 Jun 2020 18:38:49: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:38:49: #2 You may need to consider one of the other alternative d(s): 3,78,96 WARNING @ Sun, 21 Jun 2020 18:38:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:38:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:38:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:38:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:38:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:38:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.05_summits.bed INFO @ Sun, 21 Jun 2020 18:38:53: Done! pass1 - making usageList (295 chroms): 1 millis pass2 - checking and writing primary data (1198 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:38:54: 6000000 INFO @ Sun, 21 Jun 2020 18:39:00: 7000000 INFO @ Sun, 21 Jun 2020 18:39:06: 8000000 INFO @ Sun, 21 Jun 2020 18:39:08: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:39:12: 9000000 INFO @ Sun, 21 Jun 2020 18:39:15: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:39:15: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:39:15: #1 total tags in treatment: 9512879 INFO @ Sun, 21 Jun 2020 18:39:15: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:39:15: #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 18:39:16: #1 tags after filtering in treatment: 9512741 INFO @ Sun, 21 Jun 2020 18:39:16: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:39:16: #1 finished! INFO @ Sun, 21 Jun 2020 18:39:16: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:39:16: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:39:17: #2 number of paired peaks: 791 WARNING @ Sun, 21 Jun 2020 18:39:17: Fewer paired peaks (791) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 791 pairs to build model! INFO @ Sun, 21 Jun 2020 18:39:17: start model_add_line... INFO @ Sun, 21 Jun 2020 18:39:17: start X-correlation... INFO @ Sun, 21 Jun 2020 18:39:17: end of X-cor INFO @ Sun, 21 Jun 2020 18:39:17: #2 finished! INFO @ Sun, 21 Jun 2020 18:39:17: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 18:39:17: #2 alternative fragment length(s) may be 3,78,96 bps INFO @ Sun, 21 Jun 2020 18:39:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.20_model.r WARNING @ Sun, 21 Jun 2020 18:39:17: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:39:17: #2 You may need to consider one of the other alternative d(s): 3,78,96 WARNING @ Sun, 21 Jun 2020 18:39:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 18:39:17: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:39:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:39:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:39:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:39:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.10_summits.bed INFO @ Sun, 21 Jun 2020 18:39:18: Done! pass1 - making usageList (141 chroms): 1 millis pass2 - checking and writing primary data (436 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:39:35: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:39:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:39:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:39:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433371/SRX1433371.20_summits.bed INFO @ Sun, 21 Jun 2020 18:39:46: Done! pass1 - making usageList (78 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 5 millis CompletedMACS2peakCalling