Job ID = 6529291 SRX = SRX1300693 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: 00:06:19 22170985 reads; of these: 22170985 (100.00%) were unpaired; of these: 1091743 (4.92%) aligned 0 times 14922187 (67.31%) aligned exactly 1 time 6157055 (27.77%) aligned >1 times 95.08% overall alignment rate Time searching: 00:06:19 Overall time: 00:06:19 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] 2785131 / 21079242 = 0.1321 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 01:55:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.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 01:55:06: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:55:06: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:55:12: 1000000 INFO @ Tue, 30 Jun 2020 01:55:18: 2000000 INFO @ Tue, 30 Jun 2020 01:55:24: 3000000 INFO @ Tue, 30 Jun 2020 01:55:31: 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 01:55:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.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 01:55:36: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:55:36: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:55:37: 5000000 INFO @ Tue, 30 Jun 2020 01:55:41: 1000000 INFO @ Tue, 30 Jun 2020 01:55:43: 6000000 INFO @ Tue, 30 Jun 2020 01:55:47: 2000000 INFO @ Tue, 30 Jun 2020 01:55:50: 7000000 INFO @ Tue, 30 Jun 2020 01:55:53: 3000000 INFO @ Tue, 30 Jun 2020 01:55:56: 8000000 INFO @ Tue, 30 Jun 2020 01:55:59: 4000000 INFO @ Tue, 30 Jun 2020 01:56:02: 9000000 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 01:56:05: 5000000 INFO @ Tue, 30 Jun 2020 01:56:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.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 01:56:06: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:56:06: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:56:09: 10000000 INFO @ Tue, 30 Jun 2020 01:56:11: 6000000 INFO @ Tue, 30 Jun 2020 01:56:12: 1000000 INFO @ Tue, 30 Jun 2020 01:56:15: 11000000 INFO @ Tue, 30 Jun 2020 01:56:17: 7000000 INFO @ Tue, 30 Jun 2020 01:56:18: 2000000 INFO @ Tue, 30 Jun 2020 01:56:22: 12000000 INFO @ Tue, 30 Jun 2020 01:56:23: 8000000 INFO @ Tue, 30 Jun 2020 01:56:24: 3000000 INFO @ Tue, 30 Jun 2020 01:56:28: 13000000 INFO @ Tue, 30 Jun 2020 01:56:29: 9000000 INFO @ Tue, 30 Jun 2020 01:56:30: 4000000 INFO @ Tue, 30 Jun 2020 01:56:35: 10000000 INFO @ Tue, 30 Jun 2020 01:56:35: 14000000 INFO @ Tue, 30 Jun 2020 01:56:36: 5000000 INFO @ Tue, 30 Jun 2020 01:56:40: 11000000 INFO @ Tue, 30 Jun 2020 01:56:42: 15000000 INFO @ Tue, 30 Jun 2020 01:56:42: 6000000 INFO @ Tue, 30 Jun 2020 01:56:46: 12000000 INFO @ Tue, 30 Jun 2020 01:56:48: 7000000 INFO @ Tue, 30 Jun 2020 01:56:48: 16000000 INFO @ Tue, 30 Jun 2020 01:56:52: 13000000 INFO @ Tue, 30 Jun 2020 01:56:54: 8000000 INFO @ Tue, 30 Jun 2020 01:56:55: 17000000 INFO @ Tue, 30 Jun 2020 01:56:59: 14000000 INFO @ Tue, 30 Jun 2020 01:57:00: 9000000 INFO @ Tue, 30 Jun 2020 01:57:02: 18000000 INFO @ Tue, 30 Jun 2020 01:57:04: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:57:04: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:57:04: #1 total tags in treatment: 18294111 INFO @ Tue, 30 Jun 2020 01:57:04: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:57:04: #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 01:57:04: #1 tags after filtering in treatment: 18294111 INFO @ Tue, 30 Jun 2020 01:57:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:57:04: #1 finished! INFO @ Tue, 30 Jun 2020 01:57:04: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:57:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:57:05: 15000000 INFO @ Tue, 30 Jun 2020 01:57:06: #2 number of paired peaks: 587 WARNING @ Tue, 30 Jun 2020 01:57:06: Fewer paired peaks (587) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 587 pairs to build model! INFO @ Tue, 30 Jun 2020 01:57:06: start model_add_line... INFO @ Tue, 30 Jun 2020 01:57:06: start X-correlation... INFO @ Tue, 30 Jun 2020 01:57:06: end of X-cor INFO @ Tue, 30 Jun 2020 01:57:06: #2 finished! INFO @ Tue, 30 Jun 2020 01:57:06: #2 predicted fragment length is 37 bps INFO @ Tue, 30 Jun 2020 01:57:06: #2 alternative fragment length(s) may be 2,37 bps INFO @ Tue, 30 Jun 2020 01:57:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.05_model.r WARNING @ Tue, 30 Jun 2020 01:57:06: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:57:06: #2 You may need to consider one of the other alternative d(s): 2,37 WARNING @ Tue, 30 Jun 2020 01:57:06: #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 01:57:06: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:57:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:57:06: 10000000 INFO @ Tue, 30 Jun 2020 01:57:11: 16000000 INFO @ Tue, 30 Jun 2020 01:57:12: 11000000 INFO @ Tue, 30 Jun 2020 01:57:17: 17000000 INFO @ Tue, 30 Jun 2020 01:57:18: 12000000 INFO @ Tue, 30 Jun 2020 01:57:23: 18000000 INFO @ Tue, 30 Jun 2020 01:57:24: 13000000 INFO @ Tue, 30 Jun 2020 01:57:25: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:57:25: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:57:25: #1 total tags in treatment: 18294111 INFO @ Tue, 30 Jun 2020 01:57:25: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:57:25: #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 01:57:26: #1 tags after filtering in treatment: 18294111 INFO @ Tue, 30 Jun 2020 01:57:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:57:26: #1 finished! INFO @ Tue, 30 Jun 2020 01:57:26: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:57:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:57:27: #2 number of paired peaks: 587 WARNING @ Tue, 30 Jun 2020 01:57:27: Fewer paired peaks (587) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 587 pairs to build model! INFO @ Tue, 30 Jun 2020 01:57:27: start model_add_line... INFO @ Tue, 30 Jun 2020 01:57:27: start X-correlation... INFO @ Tue, 30 Jun 2020 01:57:27: end of X-cor INFO @ Tue, 30 Jun 2020 01:57:27: #2 finished! INFO @ Tue, 30 Jun 2020 01:57:27: #2 predicted fragment length is 37 bps INFO @ Tue, 30 Jun 2020 01:57:27: #2 alternative fragment length(s) may be 2,37 bps INFO @ Tue, 30 Jun 2020 01:57:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.10_model.r WARNING @ Tue, 30 Jun 2020 01:57:27: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:57:27: #2 You may need to consider one of the other alternative d(s): 2,37 WARNING @ Tue, 30 Jun 2020 01:57:27: #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 01:57:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:57:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:57:29: 14000000 INFO @ Tue, 30 Jun 2020 01:57:35: 15000000 INFO @ Tue, 30 Jun 2020 01:57:41: 16000000 INFO @ Tue, 30 Jun 2020 01:57:42: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:57:47: 17000000 INFO @ Tue, 30 Jun 2020 01:57:52: 18000000 INFO @ Tue, 30 Jun 2020 01:57:54: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:57:54: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:57:54: #1 total tags in treatment: 18294111 INFO @ Tue, 30 Jun 2020 01:57:54: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:57:54: #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 01:57:55: #1 tags after filtering in treatment: 18294111 INFO @ Tue, 30 Jun 2020 01:57:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:57:55: #1 finished! INFO @ Tue, 30 Jun 2020 01:57:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:57:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:57:56: #2 number of paired peaks: 587 WARNING @ Tue, 30 Jun 2020 01:57:56: Fewer paired peaks (587) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 587 pairs to build model! INFO @ Tue, 30 Jun 2020 01:57:56: start model_add_line... INFO @ Tue, 30 Jun 2020 01:57:56: start X-correlation... INFO @ Tue, 30 Jun 2020 01:57:56: end of X-cor INFO @ Tue, 30 Jun 2020 01:57:56: #2 finished! INFO @ Tue, 30 Jun 2020 01:57:56: #2 predicted fragment length is 37 bps INFO @ Tue, 30 Jun 2020 01:57:56: #2 alternative fragment length(s) may be 2,37 bps INFO @ Tue, 30 Jun 2020 01:57:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.20_model.r WARNING @ Tue, 30 Jun 2020 01:57:56: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:57:56: #2 You may need to consider one of the other alternative d(s): 2,37 WARNING @ Tue, 30 Jun 2020 01:57:56: #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 01:57:56: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:57:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:58:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:58:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:58:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.05_summits.bed INFO @ Tue, 30 Jun 2020 01:58:01: Done! pass1 - making usageList (659 chroms): 1 millis pass2 - checking and writing primary data (2617 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:58:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:58:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:58:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:58:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.10_summits.bed INFO @ Tue, 30 Jun 2020 01:58:23: Done! pass1 - making usageList (525 chroms): 1 millis pass2 - checking and writing primary data (2018 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:58:32: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:58:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:58:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:58:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1300693/SRX1300693.20_summits.bed INFO @ Tue, 30 Jun 2020 01:58:50: Done! pass1 - making usageList (348 chroms): 1 millis pass2 - checking and writing primary data (848 records, 4 fields): 12 millis CompletedMACS2peakCalling