Job ID = 6529140 SRX = SRX011652 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: 00:02:57 16290068 reads; of these: 16290068 (100.00%) were unpaired; of these: 2208149 (13.56%) aligned 0 times 11935803 (73.27%) aligned exactly 1 time 2146116 (13.17%) aligned >1 times 86.44% overall alignment rate Time searching: 00:02:57 Overall time: 00:02:57 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_rmdupse_core] 853434 / 14081919 = 0.0606 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 01:31:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.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 01:31:40: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:31:40: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:31:45: 1000000 INFO @ Tue, 30 Jun 2020 01:31:50: 2000000 INFO @ Tue, 30 Jun 2020 01:31:56: 3000000 INFO @ Tue, 30 Jun 2020 01:32:01: 4000000 INFO @ Tue, 30 Jun 2020 01:32:06: 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 01:32:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.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 01:32:10: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:32:10: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:32:11: 6000000 INFO @ Tue, 30 Jun 2020 01:32:15: 1000000 INFO @ Tue, 30 Jun 2020 01:32:16: 7000000 INFO @ Tue, 30 Jun 2020 01:32:20: 2000000 INFO @ Tue, 30 Jun 2020 01:32:21: 8000000 INFO @ Tue, 30 Jun 2020 01:32:26: 3000000 INFO @ Tue, 30 Jun 2020 01:32:26: 9000000 INFO @ Tue, 30 Jun 2020 01:32:31: 10000000 INFO @ Tue, 30 Jun 2020 01:32:31: 4000000 INFO @ Tue, 30 Jun 2020 01:32:36: 11000000 INFO @ Tue, 30 Jun 2020 01:32:36: 5000000 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 01:32:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.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 01:32:40: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:32:40: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:32:42: 6000000 INFO @ Tue, 30 Jun 2020 01:32:42: 12000000 INFO @ Tue, 30 Jun 2020 01:32:46: 1000000 INFO @ Tue, 30 Jun 2020 01:32:47: 13000000 INFO @ Tue, 30 Jun 2020 01:32:47: 7000000 INFO @ Tue, 30 Jun 2020 01:32:49: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:32:49: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:32:49: #1 total tags in treatment: 13228485 INFO @ Tue, 30 Jun 2020 01:32:49: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:32:49: #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 01:32:50: #1 tags after filtering in treatment: 13228483 INFO @ Tue, 30 Jun 2020 01:32:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:32:50: #1 finished! INFO @ Tue, 30 Jun 2020 01:32:50: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:32:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:32:50: #2 number of paired peaks: 104 WARNING @ Tue, 30 Jun 2020 01:32:50: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Tue, 30 Jun 2020 01:32:50: start model_add_line... INFO @ Tue, 30 Jun 2020 01:32:51: start X-correlation... INFO @ Tue, 30 Jun 2020 01:32:51: end of X-cor INFO @ Tue, 30 Jun 2020 01:32:51: #2 finished! INFO @ Tue, 30 Jun 2020 01:32:51: #2 predicted fragment length is 38 bps INFO @ Tue, 30 Jun 2020 01:32:51: #2 alternative fragment length(s) may be 38 bps INFO @ Tue, 30 Jun 2020 01:32:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.05_model.r WARNING @ Tue, 30 Jun 2020 01:32:51: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:32:51: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Tue, 30 Jun 2020 01:32:51: #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 01:32:51: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:32:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:32:51: 2000000 INFO @ Tue, 30 Jun 2020 01:32:53: 8000000 INFO @ Tue, 30 Jun 2020 01:32:57: 3000000 INFO @ Tue, 30 Jun 2020 01:32:59: 9000000 INFO @ Tue, 30 Jun 2020 01:33:03: 4000000 INFO @ Tue, 30 Jun 2020 01:33:04: 10000000 INFO @ Tue, 30 Jun 2020 01:33:08: 5000000 INFO @ Tue, 30 Jun 2020 01:33:10: 11000000 INFO @ Tue, 30 Jun 2020 01:33:14: 6000000 INFO @ Tue, 30 Jun 2020 01:33:14: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:33:16: 12000000 INFO @ Tue, 30 Jun 2020 01:33:20: 7000000 INFO @ Tue, 30 Jun 2020 01:33:22: 13000000 INFO @ Tue, 30 Jun 2020 01:33:24: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:33:24: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:33:24: #1 total tags in treatment: 13228485 INFO @ Tue, 30 Jun 2020 01:33:24: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:33:24: #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 01:33:25: #1 tags after filtering in treatment: 13228483 INFO @ Tue, 30 Jun 2020 01:33:25: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:33:25: #1 finished! INFO @ Tue, 30 Jun 2020 01:33:25: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:33:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:33:25: 8000000 INFO @ Tue, 30 Jun 2020 01:33:26: #2 number of paired peaks: 104 WARNING @ Tue, 30 Jun 2020 01:33:26: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Tue, 30 Jun 2020 01:33:26: start model_add_line... INFO @ Tue, 30 Jun 2020 01:33:26: start X-correlation... INFO @ Tue, 30 Jun 2020 01:33:26: end of X-cor INFO @ Tue, 30 Jun 2020 01:33:26: #2 finished! INFO @ Tue, 30 Jun 2020 01:33:26: #2 predicted fragment length is 38 bps INFO @ Tue, 30 Jun 2020 01:33:26: #2 alternative fragment length(s) may be 38 bps INFO @ Tue, 30 Jun 2020 01:33:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.10_model.r WARNING @ Tue, 30 Jun 2020 01:33:26: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:33:26: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Tue, 30 Jun 2020 01:33:26: #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 01:33:26: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:33:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:33:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:33:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:33:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.05_summits.bed INFO @ Tue, 30 Jun 2020 01:33:27: Done! pass1 - making usageList (127 chroms): 1 millis pass2 - checking and writing primary data (678 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:33:31: 9000000 INFO @ Tue, 30 Jun 2020 01:33:36: 10000000 INFO @ Tue, 30 Jun 2020 01:33:41: 11000000 INFO @ Tue, 30 Jun 2020 01:33:48: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:33:50: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:33:53: 13000000 INFO @ Tue, 30 Jun 2020 01:33:55: #1 tag size is determined as 36 bps INFO @ Tue, 30 Jun 2020 01:33:55: #1 tag size = 36 INFO @ Tue, 30 Jun 2020 01:33:55: #1 total tags in treatment: 13228485 INFO @ Tue, 30 Jun 2020 01:33:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:33:55: #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 01:33:55: #1 tags after filtering in treatment: 13228483 INFO @ Tue, 30 Jun 2020 01:33:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:33:55: #1 finished! INFO @ Tue, 30 Jun 2020 01:33:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:33:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:33:56: #2 number of paired peaks: 104 WARNING @ Tue, 30 Jun 2020 01:33:56: Fewer paired peaks (104) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 104 pairs to build model! INFO @ Tue, 30 Jun 2020 01:33:56: start model_add_line... INFO @ Tue, 30 Jun 2020 01:33:56: start X-correlation... INFO @ Tue, 30 Jun 2020 01:33:56: end of X-cor INFO @ Tue, 30 Jun 2020 01:33:56: #2 finished! INFO @ Tue, 30 Jun 2020 01:33:56: #2 predicted fragment length is 38 bps INFO @ Tue, 30 Jun 2020 01:33:56: #2 alternative fragment length(s) may be 38 bps INFO @ Tue, 30 Jun 2020 01:33:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.20_model.r WARNING @ Tue, 30 Jun 2020 01:33:56: #2 Since the d (38) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:33:56: #2 You may need to consider one of the other alternative d(s): 38 WARNING @ Tue, 30 Jun 2020 01:33:56: #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 01:33:56: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:33:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:34:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:34:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:34:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.10_summits.bed INFO @ Tue, 30 Jun 2020 01:34:02: Done! pass1 - making usageList (89 chroms): 1 millis pass2 - checking and writing primary data (227 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:34:20: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:34:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:34:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:34:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX011652/SRX011652.20_summits.bed INFO @ Tue, 30 Jun 2020 01:34:33: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (81 records, 4 fields): 4 millis CompletedMACS2peakCalling