Job ID = 6529944 SRX = SRX5431036 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: 00:05:13 18875551 reads; of these: 18875551 (100.00%) were unpaired; of these: 1515340 (8.03%) aligned 0 times 13376975 (70.87%) aligned exactly 1 time 3983236 (21.10%) aligned >1 times 91.97% overall alignment rate Time searching: 00:05:13 Overall time: 00:05:13 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] 1721391 / 17360211 = 0.0992 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 03:09:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.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 03:09:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:09:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:09:37: 1000000 INFO @ Tue, 30 Jun 2020 03:09:43: 2000000 INFO @ Tue, 30 Jun 2020 03:09:48: 3000000 INFO @ Tue, 30 Jun 2020 03:09:54: 4000000 INFO @ Tue, 30 Jun 2020 03:09:59: 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 @ Tue, 30 Jun 2020 03:10:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.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 03:10:02: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:02: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:10:04: 6000000 INFO @ Tue, 30 Jun 2020 03:10:08: 1000000 INFO @ Tue, 30 Jun 2020 03:10:10: 7000000 INFO @ Tue, 30 Jun 2020 03:10:13: 2000000 INFO @ Tue, 30 Jun 2020 03:10:15: 8000000 INFO @ Tue, 30 Jun 2020 03:10:19: 3000000 INFO @ Tue, 30 Jun 2020 03:10:21: 9000000 INFO @ Tue, 30 Jun 2020 03:10:24: 4000000 INFO @ Tue, 30 Jun 2020 03:10:26: 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 @ Tue, 30 Jun 2020 03:10:30: 5000000 INFO @ Tue, 30 Jun 2020 03:10:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.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 03:10:32: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:10:32: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:10:32: 11000000 INFO @ Tue, 30 Jun 2020 03:10:36: 6000000 INFO @ Tue, 30 Jun 2020 03:10:38: 12000000 INFO @ Tue, 30 Jun 2020 03:10:38: 1000000 INFO @ Tue, 30 Jun 2020 03:10:41: 7000000 INFO @ Tue, 30 Jun 2020 03:10:44: 13000000 INFO @ Tue, 30 Jun 2020 03:10:44: 2000000 INFO @ Tue, 30 Jun 2020 03:10:47: 8000000 INFO @ Tue, 30 Jun 2020 03:10:50: 14000000 INFO @ Tue, 30 Jun 2020 03:10:50: 3000000 INFO @ Tue, 30 Jun 2020 03:10:53: 9000000 INFO @ Tue, 30 Jun 2020 03:10:55: 15000000 INFO @ Tue, 30 Jun 2020 03:10:56: 4000000 INFO @ Tue, 30 Jun 2020 03:10:58: 10000000 INFO @ Tue, 30 Jun 2020 03:11:00: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:11:00: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:11:00: #1 total tags in treatment: 15638820 INFO @ Tue, 30 Jun 2020 03:11:00: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:11:00: #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 03:11:00: #1 tags after filtering in treatment: 15638817 INFO @ Tue, 30 Jun 2020 03:11:00: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:11:00: #1 finished! INFO @ Tue, 30 Jun 2020 03:11:00: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:11:00: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:11:01: #2 number of paired peaks: 311 WARNING @ Tue, 30 Jun 2020 03:11:01: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Tue, 30 Jun 2020 03:11:01: start model_add_line... INFO @ Tue, 30 Jun 2020 03:11:01: start X-correlation... INFO @ Tue, 30 Jun 2020 03:11:01: end of X-cor INFO @ Tue, 30 Jun 2020 03:11:01: #2 finished! INFO @ Tue, 30 Jun 2020 03:11:01: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 03:11:01: #2 alternative fragment length(s) may be 3,48,584 bps INFO @ Tue, 30 Jun 2020 03:11:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.05_model.r WARNING @ Tue, 30 Jun 2020 03:11:02: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:11:02: #2 You may need to consider one of the other alternative d(s): 3,48,584 WARNING @ Tue, 30 Jun 2020 03:11:02: #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 03:11:02: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:11:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:11:02: 5000000 INFO @ Tue, 30 Jun 2020 03:11:04: 11000000 INFO @ Tue, 30 Jun 2020 03:11:08: 6000000 INFO @ Tue, 30 Jun 2020 03:11:10: 12000000 INFO @ Tue, 30 Jun 2020 03:11:13: 7000000 INFO @ Tue, 30 Jun 2020 03:11:16: 13000000 INFO @ Tue, 30 Jun 2020 03:11:19: 8000000 INFO @ Tue, 30 Jun 2020 03:11:22: 14000000 INFO @ Tue, 30 Jun 2020 03:11:25: 9000000 INFO @ Tue, 30 Jun 2020 03:11:28: 15000000 INFO @ Tue, 30 Jun 2020 03:11:31: 10000000 INFO @ Tue, 30 Jun 2020 03:11:32: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:11:32: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:11:32: #1 total tags in treatment: 15638820 INFO @ Tue, 30 Jun 2020 03:11:32: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:11:32: #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 03:11:32: #1 tags after filtering in treatment: 15638817 INFO @ Tue, 30 Jun 2020 03:11:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:11:32: #1 finished! INFO @ Tue, 30 Jun 2020 03:11:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:11:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:11:34: #2 number of paired peaks: 311 WARNING @ Tue, 30 Jun 2020 03:11:34: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Tue, 30 Jun 2020 03:11:34: start model_add_line... INFO @ Tue, 30 Jun 2020 03:11:34: start X-correlation... INFO @ Tue, 30 Jun 2020 03:11:34: end of X-cor INFO @ Tue, 30 Jun 2020 03:11:34: #2 finished! INFO @ Tue, 30 Jun 2020 03:11:34: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 03:11:34: #2 alternative fragment length(s) may be 3,48,584 bps INFO @ Tue, 30 Jun 2020 03:11:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.10_model.r WARNING @ Tue, 30 Jun 2020 03:11:34: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:11:34: #2 You may need to consider one of the other alternative d(s): 3,48,584 WARNING @ Tue, 30 Jun 2020 03:11:34: #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 03:11:34: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:11:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:11:36: 11000000 INFO @ Tue, 30 Jun 2020 03:11:38: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:11:42: 12000000 INFO @ Tue, 30 Jun 2020 03:11:48: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:11:54: 14000000 INFO @ Tue, 30 Jun 2020 03:11:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:11:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:11:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.05_summits.bed INFO @ Tue, 30 Jun 2020 03:11:56: Done! pass1 - making usageList (539 chroms): 2 millis pass2 - checking and writing primary data (4295 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:11:59: 15000000 INFO @ Tue, 30 Jun 2020 03:12:04: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:12:04: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:12:04: #1 total tags in treatment: 15638820 INFO @ Tue, 30 Jun 2020 03:12:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:12:04: #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 03:12:04: #1 tags after filtering in treatment: 15638817 INFO @ Tue, 30 Jun 2020 03:12:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:12:04: #1 finished! INFO @ Tue, 30 Jun 2020 03:12:04: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:12:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:12:05: #2 number of paired peaks: 311 WARNING @ Tue, 30 Jun 2020 03:12:05: Fewer paired peaks (311) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 311 pairs to build model! INFO @ Tue, 30 Jun 2020 03:12:05: start model_add_line... INFO @ Tue, 30 Jun 2020 03:12:06: start X-correlation... INFO @ Tue, 30 Jun 2020 03:12:06: end of X-cor INFO @ Tue, 30 Jun 2020 03:12:06: #2 finished! INFO @ Tue, 30 Jun 2020 03:12:06: #2 predicted fragment length is 48 bps INFO @ Tue, 30 Jun 2020 03:12:06: #2 alternative fragment length(s) may be 3,48,584 bps INFO @ Tue, 30 Jun 2020 03:12:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.20_model.r WARNING @ Tue, 30 Jun 2020 03:12:06: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:12:06: #2 You may need to consider one of the other alternative d(s): 3,48,584 WARNING @ Tue, 30 Jun 2020 03:12:06: #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 03:12:06: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:12:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:12:09: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:12:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:12:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:12:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.10_summits.bed INFO @ Tue, 30 Jun 2020 03:12:29: Done! pass1 - making usageList (423 chroms): 1 millis pass2 - checking and writing primary data (1633 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:12:42: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:13:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:13:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:13:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5431036/SRX5431036.20_summits.bed INFO @ Tue, 30 Jun 2020 03:13:00: Done! pass1 - making usageList (216 chroms): 1 millis pass2 - checking and writing primary data (432 records, 4 fields): 8 millis CompletedMACS2peakCalling