Job ID = 6529204 SRX = SRX041393 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: 00:05:38 27341616 reads; of these: 27341616 (100.00%) were unpaired; of these: 782403 (2.86%) aligned 0 times 21709166 (79.40%) aligned exactly 1 time 4850047 (17.74%) aligned >1 times 97.14% overall alignment rate Time searching: 00:05:38 Overall time: 00:05:38 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] 3369554 / 26559213 = 0.1269 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 01:39:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.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 01:39:56: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:39:56: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:40:00: 1000000 INFO @ Tue, 30 Jun 2020 01:40:05: 2000000 INFO @ Tue, 30 Jun 2020 01:40:09: 3000000 INFO @ Tue, 30 Jun 2020 01:40:14: 4000000 INFO @ Tue, 30 Jun 2020 01:40:18: 5000000 INFO @ Tue, 30 Jun 2020 01:40:23: 6000000 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 01:40:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.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 01:40:26: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:40:26: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:40:27: 7000000 INFO @ Tue, 30 Jun 2020 01:40:31: 1000000 INFO @ Tue, 30 Jun 2020 01:40:32: 8000000 INFO @ Tue, 30 Jun 2020 01:40:36: 2000000 INFO @ Tue, 30 Jun 2020 01:40:37: 9000000 INFO @ Tue, 30 Jun 2020 01:40:40: 3000000 INFO @ Tue, 30 Jun 2020 01:40:41: 10000000 INFO @ Tue, 30 Jun 2020 01:40:45: 4000000 INFO @ Tue, 30 Jun 2020 01:40:45: 11000000 INFO @ Tue, 30 Jun 2020 01:40:50: 5000000 INFO @ Tue, 30 Jun 2020 01:40:50: 12000000 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 01:40:54: 13000000 INFO @ Tue, 30 Jun 2020 01:40:54: 6000000 INFO @ Tue, 30 Jun 2020 01:40:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.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 01:40:56: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:40:56: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:40:59: 14000000 INFO @ Tue, 30 Jun 2020 01:40:59: 7000000 INFO @ Tue, 30 Jun 2020 01:41:01: 1000000 INFO @ Tue, 30 Jun 2020 01:41:03: 15000000 INFO @ Tue, 30 Jun 2020 01:41:05: 8000000 INFO @ Tue, 30 Jun 2020 01:41:06: 2000000 INFO @ Tue, 30 Jun 2020 01:41:08: 16000000 INFO @ Tue, 30 Jun 2020 01:41:10: 9000000 INFO @ Tue, 30 Jun 2020 01:41:12: 3000000 INFO @ Tue, 30 Jun 2020 01:41:12: 17000000 INFO @ Tue, 30 Jun 2020 01:41:15: 10000000 INFO @ Tue, 30 Jun 2020 01:41:16: 18000000 INFO @ Tue, 30 Jun 2020 01:41:17: 4000000 INFO @ Tue, 30 Jun 2020 01:41:20: 11000000 INFO @ Tue, 30 Jun 2020 01:41:21: 19000000 INFO @ Tue, 30 Jun 2020 01:41:22: 5000000 INFO @ Tue, 30 Jun 2020 01:41:25: 12000000 INFO @ Tue, 30 Jun 2020 01:41:26: 20000000 INFO @ Tue, 30 Jun 2020 01:41:27: 6000000 INFO @ Tue, 30 Jun 2020 01:41:30: 13000000 INFO @ Tue, 30 Jun 2020 01:41:30: 21000000 INFO @ Tue, 30 Jun 2020 01:41:33: 7000000 INFO @ Tue, 30 Jun 2020 01:41:35: 22000000 INFO @ Tue, 30 Jun 2020 01:41:35: 14000000 INFO @ Tue, 30 Jun 2020 01:41:38: 8000000 INFO @ Tue, 30 Jun 2020 01:41:40: 23000000 INFO @ Tue, 30 Jun 2020 01:41:40: 15000000 INFO @ Tue, 30 Jun 2020 01:41:41: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:41:41: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:41:41: #1 total tags in treatment: 23189659 INFO @ Tue, 30 Jun 2020 01:41:41: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:41:41: #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 01:41:42: #1 tags after filtering in treatment: 23189654 INFO @ Tue, 30 Jun 2020 01:41:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:41:42: #1 finished! INFO @ Tue, 30 Jun 2020 01:41:42: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:41:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:41:43: 9000000 INFO @ Tue, 30 Jun 2020 01:41:43: #2 number of paired peaks: 128 WARNING @ Tue, 30 Jun 2020 01:41:43: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Tue, 30 Jun 2020 01:41:43: start model_add_line... INFO @ Tue, 30 Jun 2020 01:41:43: start X-correlation... INFO @ Tue, 30 Jun 2020 01:41:43: end of X-cor INFO @ Tue, 30 Jun 2020 01:41:43: #2 finished! INFO @ Tue, 30 Jun 2020 01:41:43: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 01:41:43: #2 alternative fragment length(s) may be 3,42,598 bps INFO @ Tue, 30 Jun 2020 01:41:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.05_model.r WARNING @ Tue, 30 Jun 2020 01:41:43: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:41:43: #2 You may need to consider one of the other alternative d(s): 3,42,598 WARNING @ Tue, 30 Jun 2020 01:41:43: #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 01:41:43: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:41:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:41:45: 16000000 INFO @ Tue, 30 Jun 2020 01:41:48: 10000000 INFO @ Tue, 30 Jun 2020 01:41:50: 17000000 INFO @ Tue, 30 Jun 2020 01:41:53: 11000000 INFO @ Tue, 30 Jun 2020 01:41:56: 18000000 INFO @ Tue, 30 Jun 2020 01:41:58: 12000000 INFO @ Tue, 30 Jun 2020 01:42:01: 19000000 INFO @ Tue, 30 Jun 2020 01:42:03: 13000000 INFO @ Tue, 30 Jun 2020 01:42:07: 20000000 INFO @ Tue, 30 Jun 2020 01:42:08: 14000000 INFO @ Tue, 30 Jun 2020 01:42:12: 21000000 INFO @ Tue, 30 Jun 2020 01:42:13: 15000000 INFO @ Tue, 30 Jun 2020 01:42:17: 22000000 INFO @ Tue, 30 Jun 2020 01:42:18: 16000000 INFO @ Tue, 30 Jun 2020 01:42:21: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:42:22: 23000000 INFO @ Tue, 30 Jun 2020 01:42:23: 17000000 INFO @ Tue, 30 Jun 2020 01:42:23: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:42:23: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:42:23: #1 total tags in treatment: 23189659 INFO @ Tue, 30 Jun 2020 01:42:23: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:42:23: #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 01:42:24: #1 tags after filtering in treatment: 23189654 INFO @ Tue, 30 Jun 2020 01:42:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:42:24: #1 finished! INFO @ Tue, 30 Jun 2020 01:42:24: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:42:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:42:26: #2 number of paired peaks: 128 WARNING @ Tue, 30 Jun 2020 01:42:26: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Tue, 30 Jun 2020 01:42:26: start model_add_line... INFO @ Tue, 30 Jun 2020 01:42:26: start X-correlation... INFO @ Tue, 30 Jun 2020 01:42:26: end of X-cor INFO @ Tue, 30 Jun 2020 01:42:26: #2 finished! INFO @ Tue, 30 Jun 2020 01:42:26: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 01:42:26: #2 alternative fragment length(s) may be 3,42,598 bps INFO @ Tue, 30 Jun 2020 01:42:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.10_model.r WARNING @ Tue, 30 Jun 2020 01:42:26: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:42:26: #2 You may need to consider one of the other alternative d(s): 3,42,598 WARNING @ Tue, 30 Jun 2020 01:42:26: #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 01:42:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:42:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:42:28: 18000000 INFO @ Tue, 30 Jun 2020 01:42:33: 19000000 INFO @ Tue, 30 Jun 2020 01:42:38: 20000000 INFO @ Tue, 30 Jun 2020 01:42:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:42:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:42:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.05_summits.bed INFO @ Tue, 30 Jun 2020 01:42:40: Done! pass1 - making usageList (439 chroms): 1 millis pass2 - checking and writing primary data (1612 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:42:42: 21000000 INFO @ Tue, 30 Jun 2020 01:42:47: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:42:52: 23000000 INFO @ Tue, 30 Jun 2020 01:42:53: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:42:53: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:42:53: #1 total tags in treatment: 23189659 INFO @ Tue, 30 Jun 2020 01:42:53: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:42:53: #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 01:42:54: #1 tags after filtering in treatment: 23189654 INFO @ Tue, 30 Jun 2020 01:42:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:42:54: #1 finished! INFO @ Tue, 30 Jun 2020 01:42:54: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:42:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:42:55: #2 number of paired peaks: 128 WARNING @ Tue, 30 Jun 2020 01:42:55: Fewer paired peaks (128) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 128 pairs to build model! INFO @ Tue, 30 Jun 2020 01:42:55: start model_add_line... INFO @ Tue, 30 Jun 2020 01:42:56: start X-correlation... INFO @ Tue, 30 Jun 2020 01:42:56: end of X-cor INFO @ Tue, 30 Jun 2020 01:42:56: #2 finished! INFO @ Tue, 30 Jun 2020 01:42:56: #2 predicted fragment length is 42 bps INFO @ Tue, 30 Jun 2020 01:42:56: #2 alternative fragment length(s) may be 3,42,598 bps INFO @ Tue, 30 Jun 2020 01:42:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.20_model.r WARNING @ Tue, 30 Jun 2020 01:42:56: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:42:56: #2 You may need to consider one of the other alternative d(s): 3,42,598 WARNING @ Tue, 30 Jun 2020 01:42:56: #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 01:42:56: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:42:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:43:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:43:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:43:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:43:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.10_summits.bed INFO @ Tue, 30 Jun 2020 01:43:24: Done! pass1 - making usageList (225 chroms): 1 millis pass2 - checking and writing primary data (605 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:43:33: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:43:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:43:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:43:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX041393/SRX041393.20_summits.bed INFO @ Tue, 30 Jun 2020 01:43:53: Done! pass1 - making usageList (87 chroms): 1 millis pass2 - checking and writing primary data (203 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。