Job ID = 6454123 SRX = SRX1837975 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:40:10 prefetch.2.10.7: 1) Downloading 'SRR3658916'... 2020-06-21T09:40:10 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:44:08 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:44:08 prefetch.2.10.7: 1) 'SRR3658916' was downloaded successfully 2020-06-21T09:44:08 prefetch.2.10.7: 'SRR3658916' has 0 unresolved dependencies Read 12722724 spots for SRR3658916/SRR3658916.sra Written 12722724 spots for SRR3658916/SRR3658916.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: 00:11:54 12722724 reads; of these: 12722724 (100.00%) were unpaired; of these: 1828206 (14.37%) aligned 0 times 8951122 (70.36%) aligned exactly 1 time 1943396 (15.27%) aligned >1 times 85.63% overall alignment rate Time searching: 00:11:54 Overall time: 00:11:54 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] 3197994 / 10894518 = 0.2935 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 19:02:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.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 19:02:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:02:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:02:35: 1000000 INFO @ Sun, 21 Jun 2020 19:02:43: 2000000 INFO @ Sun, 21 Jun 2020 19:02:52: 3000000 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 19:02:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.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 19:02:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:02:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:01: 4000000 INFO @ Sun, 21 Jun 2020 19:03:06: 1000000 INFO @ Sun, 21 Jun 2020 19:03:10: 5000000 INFO @ Sun, 21 Jun 2020 19:03:17: 2000000 INFO @ Sun, 21 Jun 2020 19:03:19: 6000000 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 19:03:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.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 19:03:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:03:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:03:27: 3000000 INFO @ Sun, 21 Jun 2020 19:03:28: 7000000 INFO @ Sun, 21 Jun 2020 19:03:35: #1 tag size is determined as 148 bps INFO @ Sun, 21 Jun 2020 19:03:35: #1 tag size = 148 INFO @ Sun, 21 Jun 2020 19:03:35: #1 total tags in treatment: 7696524 INFO @ Sun, 21 Jun 2020 19:03:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:03:35: #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 19:03:36: #1 tags after filtering in treatment: 7696466 INFO @ Sun, 21 Jun 2020 19:03:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:03:36: #1 finished! INFO @ Sun, 21 Jun 2020 19:03:36: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:03:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:03:37: #2 number of paired peaks: 4103 INFO @ Sun, 21 Jun 2020 19:03:37: start model_add_line... INFO @ Sun, 21 Jun 2020 19:03:37: start X-correlation... INFO @ Sun, 21 Jun 2020 19:03:37: end of X-cor INFO @ Sun, 21 Jun 2020 19:03:37: #2 finished! INFO @ Sun, 21 Jun 2020 19:03:37: #2 predicted fragment length is 190 bps INFO @ Sun, 21 Jun 2020 19:03:37: #2 alternative fragment length(s) may be 190 bps INFO @ Sun, 21 Jun 2020 19:03:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.05_model.r WARNING @ Sun, 21 Jun 2020 19:03:37: #2 Since the d (190) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:03:37: #2 You may need to consider one of the other alternative d(s): 190 WARNING @ Sun, 21 Jun 2020 19:03:37: #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 19:03:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:03:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:03:38: 1000000 INFO @ Sun, 21 Jun 2020 19:03:39: 4000000 INFO @ Sun, 21 Jun 2020 19:03:50: 2000000 INFO @ Sun, 21 Jun 2020 19:03:51: 5000000 INFO @ Sun, 21 Jun 2020 19:04:01: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:04:02: 3000000 INFO @ Sun, 21 Jun 2020 19:04:03: 6000000 INFO @ Sun, 21 Jun 2020 19:04:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:04:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:04:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.05_summits.bed INFO @ Sun, 21 Jun 2020 19:04:11: Done! pass1 - making usageList (470 chroms): 3 millis pass2 - checking and writing primary data (10804 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:04:14: 4000000 INFO @ Sun, 21 Jun 2020 19:04:15: 7000000 INFO @ Sun, 21 Jun 2020 19:04:24: #1 tag size is determined as 148 bps INFO @ Sun, 21 Jun 2020 19:04:24: #1 tag size = 148 INFO @ Sun, 21 Jun 2020 19:04:24: #1 total tags in treatment: 7696524 INFO @ Sun, 21 Jun 2020 19:04:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:24: #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 19:04:24: #1 tags after filtering in treatment: 7696466 INFO @ Sun, 21 Jun 2020 19:04:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:24: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:24: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:04:25: 5000000 INFO @ Sun, 21 Jun 2020 19:04:25: #2 number of paired peaks: 4103 INFO @ Sun, 21 Jun 2020 19:04:25: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:25: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:25: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:25: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:25: #2 predicted fragment length is 190 bps INFO @ Sun, 21 Jun 2020 19:04:25: #2 alternative fragment length(s) may be 190 bps INFO @ Sun, 21 Jun 2020 19:04:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.10_model.r WARNING @ Sun, 21 Jun 2020 19:04:25: #2 Since the d (190) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:04:25: #2 You may need to consider one of the other alternative d(s): 190 WARNING @ Sun, 21 Jun 2020 19:04:25: #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 19:04:25: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:04:36: 6000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:04:48: 7000000 INFO @ Sun, 21 Jun 2020 19:04:50: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:04:56: #1 tag size is determined as 148 bps INFO @ Sun, 21 Jun 2020 19:04:56: #1 tag size = 148 INFO @ Sun, 21 Jun 2020 19:04:56: #1 total tags in treatment: 7696524 INFO @ Sun, 21 Jun 2020 19:04:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:04:56: #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 19:04:56: #1 tags after filtering in treatment: 7696466 INFO @ Sun, 21 Jun 2020 19:04:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:04:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:04:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:04:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:04:57: #2 number of paired peaks: 4103 INFO @ Sun, 21 Jun 2020 19:04:57: start model_add_line... INFO @ Sun, 21 Jun 2020 19:04:57: start X-correlation... INFO @ Sun, 21 Jun 2020 19:04:57: end of X-cor INFO @ Sun, 21 Jun 2020 19:04:57: #2 finished! INFO @ Sun, 21 Jun 2020 19:04:57: #2 predicted fragment length is 190 bps INFO @ Sun, 21 Jun 2020 19:04:57: #2 alternative fragment length(s) may be 190 bps INFO @ Sun, 21 Jun 2020 19:04:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.20_model.r WARNING @ Sun, 21 Jun 2020 19:04:57: #2 Since the d (190) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:04:57: #2 You may need to consider one of the other alternative d(s): 190 WARNING @ Sun, 21 Jun 2020 19:04:57: #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 19:04:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:04:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:05:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.10_summits.bed INFO @ Sun, 21 Jun 2020 19:05:00: Done! pass1 - making usageList (353 chroms): 2 millis pass2 - checking and writing primary data (6690 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:05:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:05:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:05:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:05:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1837975/SRX1837975.20_summits.bed INFO @ Sun, 21 Jun 2020 19:05:32: Done! pass1 - making usageList (227 chroms): 2 millis pass2 - checking and writing primary data (3707 records, 4 fields): 17 millis CompletedMACS2peakCalling