Job ID = 6530104 SRX = SRX969915 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: 00:00:01 Multiseed full-index search: 00:07:30 26029709 reads; of these: 26029709 (100.00%) were unpaired; of these: 874476 (3.36%) aligned 0 times 18853453 (72.43%) aligned exactly 1 time 6301780 (24.21%) aligned >1 times 96.64% overall alignment rate Time searching: 00:07:31 Overall time: 00:07:31 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] 3837653 / 25155233 = 0.1526 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, 30 Jun 2020 03:37:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.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, 30 Jun 2020 03:37:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:37:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:37:09: 1000000 INFO @ Tue, 30 Jun 2020 03:37:16: 2000000 INFO @ Tue, 30 Jun 2020 03:37:24: 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 @ Tue, 30 Jun 2020 03:37:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.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, 30 Jun 2020 03:37:31: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:37:31: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:37:31: 4000000 INFO @ Tue, 30 Jun 2020 03:37:39: 1000000 INFO @ Tue, 30 Jun 2020 03:37:39: 5000000 INFO @ Tue, 30 Jun 2020 03:37:47: 2000000 INFO @ Tue, 30 Jun 2020 03:37:47: 6000000 INFO @ Tue, 30 Jun 2020 03:37:55: 3000000 INFO @ Tue, 30 Jun 2020 03:37:55: 7000000 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, 30 Jun 2020 03:38:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.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, 30 Jun 2020 03:38:01: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:38:01: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:38:03: 8000000 INFO @ Tue, 30 Jun 2020 03:38:03: 4000000 INFO @ Tue, 30 Jun 2020 03:38:09: 1000000 INFO @ Tue, 30 Jun 2020 03:38:12: 9000000 INFO @ Tue, 30 Jun 2020 03:38:12: 5000000 INFO @ Tue, 30 Jun 2020 03:38:17: 2000000 INFO @ Tue, 30 Jun 2020 03:38:20: 10000000 INFO @ Tue, 30 Jun 2020 03:38:20: 6000000 INFO @ Tue, 30 Jun 2020 03:38:25: 3000000 INFO @ Tue, 30 Jun 2020 03:38:29: 11000000 INFO @ Tue, 30 Jun 2020 03:38:29: 7000000 INFO @ Tue, 30 Jun 2020 03:38:33: 4000000 INFO @ Tue, 30 Jun 2020 03:38:38: 8000000 INFO @ Tue, 30 Jun 2020 03:38:38: 12000000 INFO @ Tue, 30 Jun 2020 03:38:42: 5000000 INFO @ Tue, 30 Jun 2020 03:38:46: 9000000 INFO @ Tue, 30 Jun 2020 03:38:47: 13000000 INFO @ Tue, 30 Jun 2020 03:38:50: 6000000 INFO @ Tue, 30 Jun 2020 03:38:55: 10000000 INFO @ Tue, 30 Jun 2020 03:38:55: 14000000 INFO @ Tue, 30 Jun 2020 03:38:59: 7000000 INFO @ Tue, 30 Jun 2020 03:39:03: 11000000 INFO @ Tue, 30 Jun 2020 03:39:04: 15000000 INFO @ Tue, 30 Jun 2020 03:39:08: 8000000 INFO @ Tue, 30 Jun 2020 03:39:12: 12000000 INFO @ Tue, 30 Jun 2020 03:39:12: 16000000 INFO @ Tue, 30 Jun 2020 03:39:17: 9000000 INFO @ Tue, 30 Jun 2020 03:39:21: 13000000 INFO @ Tue, 30 Jun 2020 03:39:21: 17000000 INFO @ Tue, 30 Jun 2020 03:39:27: 10000000 INFO @ Tue, 30 Jun 2020 03:39:29: 14000000 INFO @ Tue, 30 Jun 2020 03:39:30: 18000000 INFO @ Tue, 30 Jun 2020 03:39:36: 11000000 INFO @ Tue, 30 Jun 2020 03:39:38: 15000000 INFO @ Tue, 30 Jun 2020 03:39:39: 19000000 INFO @ Tue, 30 Jun 2020 03:39:45: 12000000 INFO @ Tue, 30 Jun 2020 03:39:47: 16000000 INFO @ Tue, 30 Jun 2020 03:39:48: 20000000 INFO @ Tue, 30 Jun 2020 03:39:54: 13000000 INFO @ Tue, 30 Jun 2020 03:39:56: 17000000 INFO @ Tue, 30 Jun 2020 03:39:57: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:40:00: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:40:00: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:40:00: #1 total tags in treatment: 21317580 INFO @ Tue, 30 Jun 2020 03:40:00: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:40:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:40:01: #1 tags after filtering in treatment: 21317574 INFO @ Tue, 30 Jun 2020 03:40:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:40:01: #1 finished! INFO @ Tue, 30 Jun 2020 03:40:01: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:40:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:40:02: #2 number of paired peaks: 187 WARNING @ Tue, 30 Jun 2020 03:40:02: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Tue, 30 Jun 2020 03:40:02: start model_add_line... INFO @ Tue, 30 Jun 2020 03:40:03: start X-correlation... INFO @ Tue, 30 Jun 2020 03:40:03: end of X-cor INFO @ Tue, 30 Jun 2020 03:40:03: #2 finished! INFO @ Tue, 30 Jun 2020 03:40:03: #2 predicted fragment length is 84 bps INFO @ Tue, 30 Jun 2020 03:40:03: #2 alternative fragment length(s) may be 3,84 bps INFO @ Tue, 30 Jun 2020 03:40:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.05_model.r WARNING @ Tue, 30 Jun 2020 03:40:03: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:40:03: #2 You may need to consider one of the other alternative d(s): 3,84 WARNING @ Tue, 30 Jun 2020 03:40:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:40:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:40:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:40:03: 14000000 INFO @ Tue, 30 Jun 2020 03:40:05: 18000000 INFO @ Tue, 30 Jun 2020 03:40:12: 15000000 INFO @ Tue, 30 Jun 2020 03:40:14: 19000000 INFO @ Tue, 30 Jun 2020 03:40:21: 16000000 INFO @ Tue, 30 Jun 2020 03:40:22: 20000000 INFO @ Tue, 30 Jun 2020 03:40:30: 17000000 INFO @ Tue, 30 Jun 2020 03:40:31: 21000000 INFO @ Tue, 30 Jun 2020 03:40:34: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:40:34: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:40:34: #1 total tags in treatment: 21317580 INFO @ Tue, 30 Jun 2020 03:40:34: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:40:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:40:35: #1 tags after filtering in treatment: 21317574 INFO @ Tue, 30 Jun 2020 03:40:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:40:35: #1 finished! INFO @ Tue, 30 Jun 2020 03:40:35: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:40:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:40:37: #2 number of paired peaks: 187 WARNING @ Tue, 30 Jun 2020 03:40:37: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Tue, 30 Jun 2020 03:40:37: start model_add_line... INFO @ Tue, 30 Jun 2020 03:40:37: start X-correlation... INFO @ Tue, 30 Jun 2020 03:40:37: end of X-cor INFO @ Tue, 30 Jun 2020 03:40:37: #2 finished! INFO @ Tue, 30 Jun 2020 03:40:37: #2 predicted fragment length is 84 bps INFO @ Tue, 30 Jun 2020 03:40:37: #2 alternative fragment length(s) may be 3,84 bps INFO @ Tue, 30 Jun 2020 03:40:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.10_model.r WARNING @ Tue, 30 Jun 2020 03:40:37: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:40:37: #2 You may need to consider one of the other alternative d(s): 3,84 WARNING @ Tue, 30 Jun 2020 03:40:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:40:37: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:40:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:40:39: 18000000 INFO @ Tue, 30 Jun 2020 03:40:39: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:40:48: 19000000 INFO @ Tue, 30 Jun 2020 03:40:57: 20000000 INFO @ Tue, 30 Jun 2020 03:40:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:40:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:40:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.05_summits.bed INFO @ Tue, 30 Jun 2020 03:40:58: Done! pass1 - making usageList (650 chroms): 2 millis pass2 - checking and writing primary data (4855 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:41:05: 21000000 INFO @ Tue, 30 Jun 2020 03:41:07: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:41:07: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:41:07: #1 total tags in treatment: 21317580 INFO @ Tue, 30 Jun 2020 03:41:07: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:41:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:41:08: #1 tags after filtering in treatment: 21317574 INFO @ Tue, 30 Jun 2020 03:41:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:41:08: #1 finished! INFO @ Tue, 30 Jun 2020 03:41:08: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:41:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:41:10: #2 number of paired peaks: 187 WARNING @ Tue, 30 Jun 2020 03:41:10: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Tue, 30 Jun 2020 03:41:10: start model_add_line... INFO @ Tue, 30 Jun 2020 03:41:10: start X-correlation... INFO @ Tue, 30 Jun 2020 03:41:10: end of X-cor INFO @ Tue, 30 Jun 2020 03:41:10: #2 finished! INFO @ Tue, 30 Jun 2020 03:41:10: #2 predicted fragment length is 84 bps INFO @ Tue, 30 Jun 2020 03:41:10: #2 alternative fragment length(s) may be 3,84 bps INFO @ Tue, 30 Jun 2020 03:41:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.20_model.r WARNING @ Tue, 30 Jun 2020 03:41:10: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:41:10: #2 You may need to consider one of the other alternative d(s): 3,84 WARNING @ Tue, 30 Jun 2020 03:41:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:41:10: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:41:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:41:13: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:41:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:41:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:41:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.10_summits.bed INFO @ Tue, 30 Jun 2020 03:41:32: Done! pass1 - making usageList (513 chroms): 1 millis pass2 - checking and writing primary data (3011 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:41:46: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:42:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:42:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:42:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX969915/SRX969915.20_summits.bed INFO @ Tue, 30 Jun 2020 03:42:05: Done! pass1 - making usageList (335 chroms): 1 millis pass2 - checking and writing primary data (1240 records, 4 fields): 20 millis CompletedMACS2peakCalling