Job ID = 6458318 SRX = SRX5011068 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:20:37 prefetch.2.10.7: 1) Downloading 'SRR8191517'... 2020-06-21T12:20:37 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:23:33 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:23:33 prefetch.2.10.7: 1) 'SRR8191517' was downloaded successfully 2020-06-21T12:23:33 prefetch.2.10.7: 'SRR8191517' has 0 unresolved dependencies Read 31207186 spots for SRR8191517/SRR8191517.sra Written 31207186 spots for SRR8191517/SRR8191517.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: 00:07:14 31207186 reads; of these: 31207186 (100.00%) were unpaired; of these: 3864246 (12.38%) aligned 0 times 21300334 (68.25%) aligned exactly 1 time 6042606 (19.36%) aligned >1 times 87.62% overall alignment rate Time searching: 00:07:14 Overall time: 00:07:14 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 12 files... [bam_rmdupse_core] 10679508 / 27342940 = 0.3906 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 21:36:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.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 21:36:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:36:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:36:58: 1000000 INFO @ Sun, 21 Jun 2020 21:37:03: 2000000 INFO @ Sun, 21 Jun 2020 21:37:08: 3000000 INFO @ Sun, 21 Jun 2020 21:37:14: 4000000 INFO @ Sun, 21 Jun 2020 21:37:19: 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 21:37:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.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 21:37:23: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:37:23: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:37:24: 6000000 INFO @ Sun, 21 Jun 2020 21:37:29: 1000000 INFO @ Sun, 21 Jun 2020 21:37:30: 7000000 INFO @ Sun, 21 Jun 2020 21:37:35: 2000000 INFO @ Sun, 21 Jun 2020 21:37:36: 8000000 INFO @ Sun, 21 Jun 2020 21:37:40: 3000000 INFO @ Sun, 21 Jun 2020 21:37:42: 9000000 INFO @ Sun, 21 Jun 2020 21:37:46: 4000000 INFO @ Sun, 21 Jun 2020 21:37:48: 10000000 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 21:37:52: 5000000 INFO @ Sun, 21 Jun 2020 21:37:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.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 21:37:53: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:37:53: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:37:53: 11000000 INFO @ Sun, 21 Jun 2020 21:37:58: 6000000 INFO @ Sun, 21 Jun 2020 21:37:59: 1000000 INFO @ Sun, 21 Jun 2020 21:37:59: 12000000 INFO @ Sun, 21 Jun 2020 21:38:04: 7000000 INFO @ Sun, 21 Jun 2020 21:38:05: 2000000 INFO @ Sun, 21 Jun 2020 21:38:05: 13000000 INFO @ Sun, 21 Jun 2020 21:38:10: 8000000 INFO @ Sun, 21 Jun 2020 21:38:11: 3000000 INFO @ Sun, 21 Jun 2020 21:38:11: 14000000 INFO @ Sun, 21 Jun 2020 21:38:16: 9000000 INFO @ Sun, 21 Jun 2020 21:38:16: 4000000 INFO @ Sun, 21 Jun 2020 21:38:17: 15000000 INFO @ Sun, 21 Jun 2020 21:38:22: 10000000 INFO @ Sun, 21 Jun 2020 21:38:22: 5000000 INFO @ Sun, 21 Jun 2020 21:38:23: 16000000 INFO @ Sun, 21 Jun 2020 21:38:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:38:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:38:27: #1 total tags in treatment: 16663432 INFO @ Sun, 21 Jun 2020 21:38:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:38:27: #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 21:38:28: 11000000 INFO @ Sun, 21 Jun 2020 21:38:28: #1 tags after filtering in treatment: 16663303 INFO @ Sun, 21 Jun 2020 21:38:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:38:28: #1 finished! INFO @ Sun, 21 Jun 2020 21:38:28: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:38:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:38:28: 6000000 INFO @ Sun, 21 Jun 2020 21:38:29: #2 number of paired peaks: 1011 INFO @ Sun, 21 Jun 2020 21:38:29: start model_add_line... INFO @ Sun, 21 Jun 2020 21:38:29: start X-correlation... INFO @ Sun, 21 Jun 2020 21:38:29: end of X-cor INFO @ Sun, 21 Jun 2020 21:38:29: #2 finished! INFO @ Sun, 21 Jun 2020 21:38:29: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 21:38:29: #2 alternative fragment length(s) may be 4,91 bps INFO @ Sun, 21 Jun 2020 21:38:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.05_model.r WARNING @ Sun, 21 Jun 2020 21:38:29: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:38:29: #2 You may need to consider one of the other alternative d(s): 4,91 WARNING @ Sun, 21 Jun 2020 21:38:29: #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 21:38:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:38:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:38:34: 12000000 INFO @ Sun, 21 Jun 2020 21:38:34: 7000000 INFO @ Sun, 21 Jun 2020 21:38:40: 13000000 INFO @ Sun, 21 Jun 2020 21:38:40: 8000000 INFO @ Sun, 21 Jun 2020 21:38:46: 14000000 INFO @ Sun, 21 Jun 2020 21:38:46: 9000000 INFO @ Sun, 21 Jun 2020 21:38:52: 15000000 INFO @ Sun, 21 Jun 2020 21:38:52: 10000000 INFO @ Sun, 21 Jun 2020 21:38:58: 16000000 INFO @ Sun, 21 Jun 2020 21:38:58: 11000000 INFO @ Sun, 21 Jun 2020 21:39:00: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:39:02: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:39:02: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:39:02: #1 total tags in treatment: 16663432 INFO @ Sun, 21 Jun 2020 21:39:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:39:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:39:02: #1 tags after filtering in treatment: 16663303 INFO @ Sun, 21 Jun 2020 21:39:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:39:02: #1 finished! INFO @ Sun, 21 Jun 2020 21:39:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:39:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:39:03: #2 number of paired peaks: 1011 INFO @ Sun, 21 Jun 2020 21:39:03: start model_add_line... INFO @ Sun, 21 Jun 2020 21:39:03: 12000000 INFO @ Sun, 21 Jun 2020 21:39:03: start X-correlation... INFO @ Sun, 21 Jun 2020 21:39:03: end of X-cor INFO @ Sun, 21 Jun 2020 21:39:03: #2 finished! INFO @ Sun, 21 Jun 2020 21:39:03: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 21:39:03: #2 alternative fragment length(s) may be 4,91 bps INFO @ Sun, 21 Jun 2020 21:39:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.10_model.r WARNING @ Sun, 21 Jun 2020 21:39:03: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:39:03: #2 You may need to consider one of the other alternative d(s): 4,91 WARNING @ Sun, 21 Jun 2020 21:39:03: #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 21:39:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:39:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:39:09: 13000000 INFO @ Sun, 21 Jun 2020 21:39:14: 14000000 INFO @ Sun, 21 Jun 2020 21:39:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:39:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:39:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.05_summits.bed INFO @ Sun, 21 Jun 2020 21:39:15: Done! pass1 - making usageList (552 chroms): 2 millis pass2 - checking and writing primary data (3717 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:39:20: 15000000 INFO @ Sun, 21 Jun 2020 21:39:25: 16000000 INFO @ Sun, 21 Jun 2020 21:39:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:39:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:39:29: #1 total tags in treatment: 16663432 INFO @ Sun, 21 Jun 2020 21:39:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:39:29: #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 21:39:29: #1 tags after filtering in treatment: 16663303 INFO @ Sun, 21 Jun 2020 21:39:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:39:29: #1 finished! INFO @ Sun, 21 Jun 2020 21:39:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:39:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:39:30: #2 number of paired peaks: 1011 INFO @ Sun, 21 Jun 2020 21:39:30: start model_add_line... INFO @ Sun, 21 Jun 2020 21:39:30: start X-correlation... INFO @ Sun, 21 Jun 2020 21:39:30: end of X-cor INFO @ Sun, 21 Jun 2020 21:39:30: #2 finished! INFO @ Sun, 21 Jun 2020 21:39:30: #2 predicted fragment length is 91 bps INFO @ Sun, 21 Jun 2020 21:39:30: #2 alternative fragment length(s) may be 4,91 bps INFO @ Sun, 21 Jun 2020 21:39:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.20_model.r WARNING @ Sun, 21 Jun 2020 21:39:30: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:39:30: #2 You may need to consider one of the other alternative d(s): 4,91 WARNING @ Sun, 21 Jun 2020 21:39:30: #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 21:39:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:39:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:39:36: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:39:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:39:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:39:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.10_summits.bed INFO @ Sun, 21 Jun 2020 21:39:51: Done! pass1 - making usageList (414 chroms): 1 millis pass2 - checking and writing primary data (2104 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:40:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:40:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:40:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:40:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011068/SRX5011068.20_summits.bed INFO @ Sun, 21 Jun 2020 21:40:17: Done! pass1 - making usageList (307 chroms): 1 millis pass2 - checking and writing primary data (1118 records, 4 fields): 9 millis CompletedMACS2peakCalling