Job ID = 6457552 SRX = SRX4669041 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:00:17 prefetch.2.10.7: 1) Downloading 'SRR7817566'... 2020-06-21T12:00:17 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:01:41 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:01:42 prefetch.2.10.7: 'SRR7817566' is valid 2020-06-21T12:01:42 prefetch.2.10.7: 1) 'SRR7817566' was downloaded successfully 2020-06-21T12:01:42 prefetch.2.10.7: 'SRR7817566' has 0 unresolved dependencies Read 10470517 spots for SRR7817566/SRR7817566.sra Written 10470517 spots for SRR7817566/SRR7817566.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: 00:02:45 10470517 reads; of these: 10470517 (100.00%) were unpaired; of these: 466823 (4.46%) aligned 0 times 6465636 (61.75%) aligned exactly 1 time 3538058 (33.79%) aligned >1 times 95.54% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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] 2103317 / 10003694 = 0.2103 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 21:07:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.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 21:07:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:07:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:07:16: 1000000 INFO @ Sun, 21 Jun 2020 21:07:21: 2000000 INFO @ Sun, 21 Jun 2020 21:07:26: 3000000 INFO @ Sun, 21 Jun 2020 21:07:32: 4000000 INFO @ Sun, 21 Jun 2020 21:07:37: 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 21:07:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.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 21:07:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:07:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:07:43: 6000000 INFO @ Sun, 21 Jun 2020 21:07:47: 1000000 INFO @ Sun, 21 Jun 2020 21:07:50: 7000000 INFO @ Sun, 21 Jun 2020 21:07:55: 2000000 INFO @ Sun, 21 Jun 2020 21:07:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:07:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:07:55: #1 total tags in treatment: 7900377 INFO @ Sun, 21 Jun 2020 21:07:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:07:55: #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 21:07:56: #1 tags after filtering in treatment: 7900324 INFO @ Sun, 21 Jun 2020 21:07:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:07:56: #1 finished! INFO @ Sun, 21 Jun 2020 21:07:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:07:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:07:56: #2 number of paired peaks: 1540 INFO @ Sun, 21 Jun 2020 21:07:56: start model_add_line... INFO @ Sun, 21 Jun 2020 21:07:57: start X-correlation... INFO @ Sun, 21 Jun 2020 21:07:57: end of X-cor INFO @ Sun, 21 Jun 2020 21:07:57: #2 finished! INFO @ Sun, 21 Jun 2020 21:07:57: #2 predicted fragment length is 90 bps INFO @ Sun, 21 Jun 2020 21:07:57: #2 alternative fragment length(s) may be 4,90 bps INFO @ Sun, 21 Jun 2020 21:07:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.05_model.r WARNING @ Sun, 21 Jun 2020 21:07:57: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:07:57: #2 You may need to consider one of the other alternative d(s): 4,90 WARNING @ Sun, 21 Jun 2020 21:07:57: #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 21:07:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:07:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:08:01: 3000000 INFO @ Sun, 21 Jun 2020 21:08:08: 4000000 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 21:08:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.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 21:08:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:08:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:08:14: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:08:15: 5000000 INFO @ Sun, 21 Jun 2020 21:08:17: 1000000 INFO @ Sun, 21 Jun 2020 21:08:22: 6000000 INFO @ Sun, 21 Jun 2020 21:08:23: 2000000 INFO @ Sun, 21 Jun 2020 21:08:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:08:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:08:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.05_summits.bed INFO @ Sun, 21 Jun 2020 21:08:23: Done! pass1 - making usageList (460 chroms): 2 millis pass2 - checking and writing primary data (5121 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:08:29: 3000000 INFO @ Sun, 21 Jun 2020 21:08:30: 7000000 INFO @ Sun, 21 Jun 2020 21:08:35: 4000000 INFO @ Sun, 21 Jun 2020 21:08:36: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:08:36: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:08:36: #1 total tags in treatment: 7900377 INFO @ Sun, 21 Jun 2020 21:08:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:08:36: #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 21:08:36: #1 tags after filtering in treatment: 7900324 INFO @ Sun, 21 Jun 2020 21:08:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:08:36: #1 finished! INFO @ Sun, 21 Jun 2020 21:08:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:08:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:08:37: #2 number of paired peaks: 1540 INFO @ Sun, 21 Jun 2020 21:08:37: start model_add_line... INFO @ Sun, 21 Jun 2020 21:08:37: start X-correlation... INFO @ Sun, 21 Jun 2020 21:08:37: end of X-cor INFO @ Sun, 21 Jun 2020 21:08:37: #2 finished! INFO @ Sun, 21 Jun 2020 21:08:37: #2 predicted fragment length is 90 bps INFO @ Sun, 21 Jun 2020 21:08:37: #2 alternative fragment length(s) may be 4,90 bps INFO @ Sun, 21 Jun 2020 21:08:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.10_model.r WARNING @ Sun, 21 Jun 2020 21:08:37: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:08:37: #2 You may need to consider one of the other alternative d(s): 4,90 WARNING @ Sun, 21 Jun 2020 21:08:37: #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 21:08:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:08:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:08:41: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:08:47: 6000000 INFO @ Sun, 21 Jun 2020 21:08:53: 7000000 INFO @ Sun, 21 Jun 2020 21:08:55: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:08:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:08:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:08:58: #1 total tags in treatment: 7900377 INFO @ Sun, 21 Jun 2020 21:08:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:08:58: #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 21:08:58: #1 tags after filtering in treatment: 7900324 INFO @ Sun, 21 Jun 2020 21:08:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:08:58: #1 finished! INFO @ Sun, 21 Jun 2020 21:08:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:08:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:08:59: #2 number of paired peaks: 1540 INFO @ Sun, 21 Jun 2020 21:08:59: start model_add_line... INFO @ Sun, 21 Jun 2020 21:08:59: start X-correlation... INFO @ Sun, 21 Jun 2020 21:08:59: end of X-cor INFO @ Sun, 21 Jun 2020 21:08:59: #2 finished! INFO @ Sun, 21 Jun 2020 21:08:59: #2 predicted fragment length is 90 bps INFO @ Sun, 21 Jun 2020 21:08:59: #2 alternative fragment length(s) may be 4,90 bps INFO @ Sun, 21 Jun 2020 21:08:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.20_model.r WARNING @ Sun, 21 Jun 2020 21:08:59: #2 Since the d (90) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:08:59: #2 You may need to consider one of the other alternative d(s): 4,90 WARNING @ Sun, 21 Jun 2020 21:08:59: #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 21:08:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:08:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:09:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:09:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:09:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.10_summits.bed INFO @ Sun, 21 Jun 2020 21:09:03: Done! pass1 - making usageList (276 chroms): 1 millis pass2 - checking and writing primary data (1673 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:09:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:09:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:09:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:09:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669041/SRX4669041.20_summits.bed INFO @ Sun, 21 Jun 2020 21:09:24: Done! pass1 - making usageList (145 chroms): 1 millis pass2 - checking and writing primary data (420 records, 4 fields): 5 millis CompletedMACS2peakCalling