Job ID = 6626990 SRX = SRX7351008 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 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: 00:09:44 26617675 reads; of these: 26617675 (100.00%) were unpaired; of these: 771776 (2.90%) aligned 0 times 17643067 (66.28%) aligned exactly 1 time 8202832 (30.82%) aligned >1 times 97.10% overall alignment rate Time searching: 00:09:44 Overall time: 00:09:44 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] 5182376 / 25845899 = 0.2005 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 @ Tue, 14 Jul 2020 09:27:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.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 @ Tue, 14 Jul 2020 09:27:03: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:27:03: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:27:10: 1000000 INFO @ Tue, 14 Jul 2020 09:27:16: 2000000 INFO @ Tue, 14 Jul 2020 09:27:23: 3000000 INFO @ Tue, 14 Jul 2020 09:27:29: 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 @ Tue, 14 Jul 2020 09:27:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.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 @ Tue, 14 Jul 2020 09:27:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:27:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:27:36: 5000000 INFO @ Tue, 14 Jul 2020 09:27:39: 1000000 INFO @ Tue, 14 Jul 2020 09:27:42: 6000000 INFO @ Tue, 14 Jul 2020 09:27:45: 2000000 INFO @ Tue, 14 Jul 2020 09:27:49: 7000000 INFO @ Tue, 14 Jul 2020 09:27:52: 3000000 INFO @ Tue, 14 Jul 2020 09:27:56: 8000000 INFO @ Tue, 14 Jul 2020 09:27:58: 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 @ Tue, 14 Jul 2020 09:28:02: 9000000 INFO @ Tue, 14 Jul 2020 09:28:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.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 @ Tue, 14 Jul 2020 09:28:03: #1 read tag files... INFO @ Tue, 14 Jul 2020 09:28:03: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 09:28:04: 5000000 INFO @ Tue, 14 Jul 2020 09:28:09: 10000000 INFO @ Tue, 14 Jul 2020 09:28:09: 1000000 INFO @ Tue, 14 Jul 2020 09:28:10: 6000000 INFO @ Tue, 14 Jul 2020 09:28:15: 11000000 INFO @ Tue, 14 Jul 2020 09:28:15: 2000000 INFO @ Tue, 14 Jul 2020 09:28:16: 7000000 INFO @ Tue, 14 Jul 2020 09:28:22: 3000000 INFO @ Tue, 14 Jul 2020 09:28:22: 12000000 INFO @ Tue, 14 Jul 2020 09:28:22: 8000000 INFO @ Tue, 14 Jul 2020 09:28:28: 9000000 INFO @ Tue, 14 Jul 2020 09:28:28: 4000000 INFO @ Tue, 14 Jul 2020 09:28:28: 13000000 INFO @ Tue, 14 Jul 2020 09:28:34: 10000000 INFO @ Tue, 14 Jul 2020 09:28:34: 5000000 INFO @ Tue, 14 Jul 2020 09:28:35: 14000000 INFO @ Tue, 14 Jul 2020 09:28:39: 11000000 INFO @ Tue, 14 Jul 2020 09:28:40: 6000000 INFO @ Tue, 14 Jul 2020 09:28:41: 15000000 INFO @ Tue, 14 Jul 2020 09:28:45: 12000000 INFO @ Tue, 14 Jul 2020 09:28:46: 7000000 INFO @ Tue, 14 Jul 2020 09:28:48: 16000000 INFO @ Tue, 14 Jul 2020 09:28:51: 13000000 INFO @ Tue, 14 Jul 2020 09:28:52: 8000000 INFO @ Tue, 14 Jul 2020 09:28:54: 17000000 INFO @ Tue, 14 Jul 2020 09:28:57: 14000000 INFO @ Tue, 14 Jul 2020 09:28:58: 9000000 INFO @ Tue, 14 Jul 2020 09:29:01: 18000000 INFO @ Tue, 14 Jul 2020 09:29:03: 15000000 INFO @ Tue, 14 Jul 2020 09:29:04: 10000000 INFO @ Tue, 14 Jul 2020 09:29:08: 19000000 INFO @ Tue, 14 Jul 2020 09:29:09: 16000000 INFO @ Tue, 14 Jul 2020 09:29:09: 11000000 INFO @ Tue, 14 Jul 2020 09:29:14: 20000000 INFO @ Tue, 14 Jul 2020 09:29:15: 17000000 INFO @ Tue, 14 Jul 2020 09:29:15: 12000000 INFO @ Tue, 14 Jul 2020 09:29:19: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:29:19: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:29:19: #1 total tags in treatment: 20663523 INFO @ Tue, 14 Jul 2020 09:29:19: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:29:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:29:19: #1 tags after filtering in treatment: 20663436 INFO @ Tue, 14 Jul 2020 09:29:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:29:19: #1 finished! INFO @ Tue, 14 Jul 2020 09:29:19: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:29:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:29:21: #2 number of paired peaks: 1022 INFO @ Tue, 14 Jul 2020 09:29:21: start model_add_line... INFO @ Tue, 14 Jul 2020 09:29:21: start X-correlation... INFO @ Tue, 14 Jul 2020 09:29:21: end of X-cor INFO @ Tue, 14 Jul 2020 09:29:21: #2 finished! INFO @ Tue, 14 Jul 2020 09:29:21: #2 predicted fragment length is 71 bps INFO @ Tue, 14 Jul 2020 09:29:21: #2 alternative fragment length(s) may be 2,71,569 bps INFO @ Tue, 14 Jul 2020 09:29:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.05_model.r WARNING @ Tue, 14 Jul 2020 09:29:21: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:29:21: #2 You may need to consider one of the other alternative d(s): 2,71,569 WARNING @ Tue, 14 Jul 2020 09:29:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:29:21: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:29:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:29:21: 18000000 INFO @ Tue, 14 Jul 2020 09:29:21: 13000000 INFO @ Tue, 14 Jul 2020 09:29:27: 19000000 INFO @ Tue, 14 Jul 2020 09:29:27: 14000000 INFO @ Tue, 14 Jul 2020 09:29:33: 20000000 INFO @ Tue, 14 Jul 2020 09:29:33: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 09:29:37: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:29:37: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:29:37: #1 total tags in treatment: 20663523 INFO @ Tue, 14 Jul 2020 09:29:37: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:29:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:29:37: #1 tags after filtering in treatment: 20663436 INFO @ Tue, 14 Jul 2020 09:29:37: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:29:37: #1 finished! INFO @ Tue, 14 Jul 2020 09:29:37: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:29:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:29:39: 16000000 INFO @ Tue, 14 Jul 2020 09:29:39: #2 number of paired peaks: 1022 INFO @ Tue, 14 Jul 2020 09:29:39: start model_add_line... INFO @ Tue, 14 Jul 2020 09:29:39: start X-correlation... INFO @ Tue, 14 Jul 2020 09:29:39: end of X-cor INFO @ Tue, 14 Jul 2020 09:29:39: #2 finished! INFO @ Tue, 14 Jul 2020 09:29:39: #2 predicted fragment length is 71 bps INFO @ Tue, 14 Jul 2020 09:29:39: #2 alternative fragment length(s) may be 2,71,569 bps INFO @ Tue, 14 Jul 2020 09:29:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.10_model.r WARNING @ Tue, 14 Jul 2020 09:29:39: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:29:39: #2 You may need to consider one of the other alternative d(s): 2,71,569 WARNING @ Tue, 14 Jul 2020 09:29:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:29:39: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:29:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:29:44: 17000000 INFO @ Tue, 14 Jul 2020 09:29:50: 18000000 INFO @ Tue, 14 Jul 2020 09:29:56: 19000000 INFO @ Tue, 14 Jul 2020 09:29:59: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:30:01: 20000000 INFO @ Tue, 14 Jul 2020 09:30:05: #1 tag size is determined as 75 bps INFO @ Tue, 14 Jul 2020 09:30:05: #1 tag size = 75 INFO @ Tue, 14 Jul 2020 09:30:05: #1 total tags in treatment: 20663523 INFO @ Tue, 14 Jul 2020 09:30:05: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 09:30:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 09:30:06: #1 tags after filtering in treatment: 20663436 INFO @ Tue, 14 Jul 2020 09:30:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 09:30:06: #1 finished! INFO @ Tue, 14 Jul 2020 09:30:06: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 09:30:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 09:30:07: #2 number of paired peaks: 1022 INFO @ Tue, 14 Jul 2020 09:30:07: start model_add_line... INFO @ Tue, 14 Jul 2020 09:30:07: start X-correlation... INFO @ Tue, 14 Jul 2020 09:30:07: end of X-cor INFO @ Tue, 14 Jul 2020 09:30:07: #2 finished! INFO @ Tue, 14 Jul 2020 09:30:07: #2 predicted fragment length is 71 bps INFO @ Tue, 14 Jul 2020 09:30:07: #2 alternative fragment length(s) may be 2,71,569 bps INFO @ Tue, 14 Jul 2020 09:30:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.20_model.r WARNING @ Tue, 14 Jul 2020 09:30:07: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 09:30:07: #2 You may need to consider one of the other alternative d(s): 2,71,569 WARNING @ Tue, 14 Jul 2020 09:30:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 09:30:07: #3 Call peaks... INFO @ Tue, 14 Jul 2020 09:30:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 09:30:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.05_peaks.xls INFO @ Tue, 14 Jul 2020 09:30:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:30:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.05_summits.bed INFO @ Tue, 14 Jul 2020 09:30:16: Done! pass1 - making usageList (624 chroms): 2 millis pass2 - checking and writing primary data (3103 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:30:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 09:30:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.10_peaks.xls INFO @ Tue, 14 Jul 2020 09:30:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:30:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.10_summits.bed INFO @ Tue, 14 Jul 2020 09:30:34: Done! pass1 - making usageList (546 chroms): 1 millis pass2 - checking and writing primary data (1899 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 09:30:45: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 09:31:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.20_peaks.xls INFO @ Tue, 14 Jul 2020 09:31:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 09:31:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX7351008/SRX7351008.20_summits.bed INFO @ Tue, 14 Jul 2020 09:31:02: Done! pass1 - making usageList (371 chroms): 1 millis pass2 - checking and writing primary data (875 records, 4 fields): 11 millis CompletedMACS2peakCalling