Job ID = 6529414 SRX = SRX2564150 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:17 37838791 reads; of these: 37838791 (100.00%) were unpaired; of these: 10618854 (28.06%) aligned 0 times 20077617 (53.06%) aligned exactly 1 time 7142320 (18.88%) aligned >1 times 71.94% overall alignment rate Time searching: 00:14:18 Overall time: 00:14:18 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] 8032861 / 27219937 = 0.2951 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 02:22:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.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 02:22:29: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:22:29: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:22:36: 1000000 INFO @ Tue, 30 Jun 2020 02:22:43: 2000000 INFO @ Tue, 30 Jun 2020 02:22:50: 3000000 INFO @ Tue, 30 Jun 2020 02:22:56: 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, 30 Jun 2020 02:22:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.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 02:22:59: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:22:59: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:23:03: 5000000 INFO @ Tue, 30 Jun 2020 02:23:07: 1000000 INFO @ Tue, 30 Jun 2020 02:23:11: 6000000 INFO @ Tue, 30 Jun 2020 02:23:14: 2000000 INFO @ Tue, 30 Jun 2020 02:23:18: 7000000 INFO @ Tue, 30 Jun 2020 02:23:21: 3000000 INFO @ Tue, 30 Jun 2020 02:23:25: 8000000 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 02:23:29: 4000000 INFO @ Tue, 30 Jun 2020 02:23:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.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 02:23:29: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:23:29: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:23:32: 9000000 INFO @ Tue, 30 Jun 2020 02:23:37: 5000000 INFO @ Tue, 30 Jun 2020 02:23:37: 1000000 INFO @ Tue, 30 Jun 2020 02:23:40: 10000000 INFO @ Tue, 30 Jun 2020 02:23:44: 6000000 INFO @ Tue, 30 Jun 2020 02:23:44: 2000000 INFO @ Tue, 30 Jun 2020 02:23:47: 11000000 INFO @ Tue, 30 Jun 2020 02:23:52: 3000000 INFO @ Tue, 30 Jun 2020 02:23:52: 7000000 INFO @ Tue, 30 Jun 2020 02:23:54: 12000000 INFO @ Tue, 30 Jun 2020 02:24:00: 8000000 INFO @ Tue, 30 Jun 2020 02:24:00: 4000000 INFO @ Tue, 30 Jun 2020 02:24:02: 13000000 INFO @ Tue, 30 Jun 2020 02:24:07: 9000000 INFO @ Tue, 30 Jun 2020 02:24:07: 5000000 INFO @ Tue, 30 Jun 2020 02:24:09: 14000000 INFO @ Tue, 30 Jun 2020 02:24:15: 10000000 INFO @ Tue, 30 Jun 2020 02:24:15: 6000000 INFO @ Tue, 30 Jun 2020 02:24:17: 15000000 INFO @ Tue, 30 Jun 2020 02:24:23: 11000000 INFO @ Tue, 30 Jun 2020 02:24:23: 7000000 INFO @ Tue, 30 Jun 2020 02:24:25: 16000000 INFO @ Tue, 30 Jun 2020 02:24:30: 12000000 INFO @ Tue, 30 Jun 2020 02:24:30: 8000000 INFO @ Tue, 30 Jun 2020 02:24:33: 17000000 INFO @ Tue, 30 Jun 2020 02:24:37: 13000000 INFO @ Tue, 30 Jun 2020 02:24:38: 9000000 INFO @ Tue, 30 Jun 2020 02:24:40: 18000000 INFO @ Tue, 30 Jun 2020 02:24:45: 14000000 INFO @ Tue, 30 Jun 2020 02:24:46: 10000000 INFO @ Tue, 30 Jun 2020 02:24:48: 19000000 INFO @ Tue, 30 Jun 2020 02:24:50: #1 tag size is determined as 72 bps INFO @ Tue, 30 Jun 2020 02:24:50: #1 tag size = 72 INFO @ Tue, 30 Jun 2020 02:24:50: #1 total tags in treatment: 19187076 INFO @ Tue, 30 Jun 2020 02:24:50: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:24:50: #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 02:24:51: #1 tags after filtering in treatment: 19187075 INFO @ Tue, 30 Jun 2020 02:24:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:24:51: #1 finished! INFO @ Tue, 30 Jun 2020 02:24:51: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:24:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:24:52: #2 number of paired peaks: 711 WARNING @ Tue, 30 Jun 2020 02:24:52: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Tue, 30 Jun 2020 02:24:52: start model_add_line... INFO @ Tue, 30 Jun 2020 02:24:52: 15000000 INFO @ Tue, 30 Jun 2020 02:24:52: start X-correlation... INFO @ Tue, 30 Jun 2020 02:24:52: end of X-cor INFO @ Tue, 30 Jun 2020 02:24:52: #2 finished! INFO @ Tue, 30 Jun 2020 02:24:52: #2 predicted fragment length is 59 bps INFO @ Tue, 30 Jun 2020 02:24:52: #2 alternative fragment length(s) may be 3,59 bps INFO @ Tue, 30 Jun 2020 02:24:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.05_model.r WARNING @ Tue, 30 Jun 2020 02:24:52: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:24:52: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Tue, 30 Jun 2020 02:24:52: #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 02:24:52: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:24:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:24:53: 11000000 INFO @ Tue, 30 Jun 2020 02:25:00: 16000000 INFO @ Tue, 30 Jun 2020 02:25:01: 12000000 INFO @ Tue, 30 Jun 2020 02:25:07: 17000000 INFO @ Tue, 30 Jun 2020 02:25:08: 13000000 INFO @ Tue, 30 Jun 2020 02:25:15: 18000000 INFO @ Tue, 30 Jun 2020 02:25:15: 14000000 INFO @ Tue, 30 Jun 2020 02:25:22: 19000000 INFO @ Tue, 30 Jun 2020 02:25:23: 15000000 INFO @ Tue, 30 Jun 2020 02:25:24: #1 tag size is determined as 72 bps INFO @ Tue, 30 Jun 2020 02:25:24: #1 tag size = 72 INFO @ Tue, 30 Jun 2020 02:25:24: #1 total tags in treatment: 19187076 INFO @ Tue, 30 Jun 2020 02:25:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:25:24: #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 02:25:25: #1 tags after filtering in treatment: 19187075 INFO @ Tue, 30 Jun 2020 02:25:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:25:25: #1 finished! INFO @ Tue, 30 Jun 2020 02:25:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:25:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:25:26: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:25:26: #2 number of paired peaks: 711 WARNING @ Tue, 30 Jun 2020 02:25:26: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Tue, 30 Jun 2020 02:25:26: start model_add_line... INFO @ Tue, 30 Jun 2020 02:25:26: start X-correlation... INFO @ Tue, 30 Jun 2020 02:25:26: end of X-cor INFO @ Tue, 30 Jun 2020 02:25:26: #2 finished! INFO @ Tue, 30 Jun 2020 02:25:26: #2 predicted fragment length is 59 bps INFO @ Tue, 30 Jun 2020 02:25:26: #2 alternative fragment length(s) may be 3,59 bps INFO @ Tue, 30 Jun 2020 02:25:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.10_model.r WARNING @ Tue, 30 Jun 2020 02:25:26: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:25:26: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Tue, 30 Jun 2020 02:25:26: #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 02:25:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:25:26: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:25:31: 16000000 INFO @ Tue, 30 Jun 2020 02:25:38: 17000000 INFO @ Tue, 30 Jun 2020 02:25:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:25:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:25:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.05_summits.bed INFO @ Tue, 30 Jun 2020 02:25:43: Done! pass1 - making usageList (695 chroms): 1 millis pass2 - checking and writing primary data (2602 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:25:44: 18000000 INFO @ Tue, 30 Jun 2020 02:25:52: 19000000 INFO @ Tue, 30 Jun 2020 02:25:53: #1 tag size is determined as 72 bps INFO @ Tue, 30 Jun 2020 02:25:53: #1 tag size = 72 INFO @ Tue, 30 Jun 2020 02:25:53: #1 total tags in treatment: 19187076 INFO @ Tue, 30 Jun 2020 02:25:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:25:53: #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 02:25:54: #1 tags after filtering in treatment: 19187075 INFO @ Tue, 30 Jun 2020 02:25:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:25:54: #1 finished! INFO @ Tue, 30 Jun 2020 02:25:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:25:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:25:56: #2 number of paired peaks: 711 WARNING @ Tue, 30 Jun 2020 02:25:56: Fewer paired peaks (711) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 711 pairs to build model! INFO @ Tue, 30 Jun 2020 02:25:56: start model_add_line... INFO @ Tue, 30 Jun 2020 02:25:56: start X-correlation... INFO @ Tue, 30 Jun 2020 02:25:56: end of X-cor INFO @ Tue, 30 Jun 2020 02:25:56: #2 finished! INFO @ Tue, 30 Jun 2020 02:25:56: #2 predicted fragment length is 59 bps INFO @ Tue, 30 Jun 2020 02:25:56: #2 alternative fragment length(s) may be 3,59 bps INFO @ Tue, 30 Jun 2020 02:25:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.20_model.r WARNING @ Tue, 30 Jun 2020 02:25:56: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:25:56: #2 You may need to consider one of the other alternative d(s): 3,59 WARNING @ Tue, 30 Jun 2020 02:25:56: #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 02:25:56: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:25:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:25:59: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:26:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:26:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:26:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.10_summits.bed INFO @ Tue, 30 Jun 2020 02:26:16: Done! pass1 - making usageList (557 chroms): 2 millis pass2 - checking and writing primary data (1731 records, 4 fields): 32 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:26:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:26:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:26:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:26:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2564150/SRX2564150.20_summits.bed INFO @ Tue, 30 Jun 2020 02:26:46: Done! pass1 - making usageList (477 chroms): 1 millis pass2 - checking and writing primary data (1387 records, 4 fields): 28 millis CompletedMACS2peakCalling