Job ID = 6530033 SRX = SRX6468492 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: 00:07:05 31202628 reads; of these: 31202628 (100.00%) were unpaired; of these: 1532909 (4.91%) aligned 0 times 24725360 (79.24%) aligned exactly 1 time 4944359 (15.85%) aligned >1 times 95.09% overall alignment rate Time searching: 00:07:05 Overall time: 00:07:05 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 16 files... [bam_rmdupse_core] 14376396 / 29669719 = 0.4845 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 03:12:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.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 03:12:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:12:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:12:32: 1000000 INFO @ Tue, 30 Jun 2020 03:12:38: 2000000 INFO @ Tue, 30 Jun 2020 03:12:44: 3000000 INFO @ Tue, 30 Jun 2020 03:12:51: 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 03:12:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.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 03:12:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:12:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:12:57: 5000000 INFO @ Tue, 30 Jun 2020 03:13:03: 1000000 INFO @ Tue, 30 Jun 2020 03:13:04: 6000000 INFO @ Tue, 30 Jun 2020 03:13:10: 2000000 INFO @ Tue, 30 Jun 2020 03:13:11: 7000000 INFO @ Tue, 30 Jun 2020 03:13:17: 3000000 INFO @ Tue, 30 Jun 2020 03:13:18: 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 03:13:24: 4000000 INFO @ Tue, 30 Jun 2020 03:13:25: 9000000 INFO @ Tue, 30 Jun 2020 03:13:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.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 03:13:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:13:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:13:31: 5000000 INFO @ Tue, 30 Jun 2020 03:13:32: 1000000 INFO @ Tue, 30 Jun 2020 03:13:32: 10000000 INFO @ Tue, 30 Jun 2020 03:13:38: 6000000 INFO @ Tue, 30 Jun 2020 03:13:38: 2000000 INFO @ Tue, 30 Jun 2020 03:13:39: 11000000 INFO @ Tue, 30 Jun 2020 03:13:45: 3000000 INFO @ Tue, 30 Jun 2020 03:13:46: 7000000 INFO @ Tue, 30 Jun 2020 03:13:47: 12000000 INFO @ Tue, 30 Jun 2020 03:13:51: 4000000 INFO @ Tue, 30 Jun 2020 03:13:53: 8000000 INFO @ Tue, 30 Jun 2020 03:13:55: 13000000 INFO @ Tue, 30 Jun 2020 03:13:58: 5000000 INFO @ Tue, 30 Jun 2020 03:14:00: 9000000 INFO @ Tue, 30 Jun 2020 03:14:02: 14000000 INFO @ Tue, 30 Jun 2020 03:14:04: 6000000 INFO @ Tue, 30 Jun 2020 03:14:07: 10000000 INFO @ Tue, 30 Jun 2020 03:14:09: 15000000 INFO @ Tue, 30 Jun 2020 03:14:10: 7000000 INFO @ Tue, 30 Jun 2020 03:14:11: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:14:11: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:14:11: #1 total tags in treatment: 15293323 INFO @ Tue, 30 Jun 2020 03:14:11: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:14:11: #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 03:14:12: #1 tags after filtering in treatment: 15293322 INFO @ Tue, 30 Jun 2020 03:14:12: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:14:12: #1 finished! INFO @ Tue, 30 Jun 2020 03:14:12: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:14:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:14:13: #2 number of paired peaks: 139 WARNING @ Tue, 30 Jun 2020 03:14:13: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Tue, 30 Jun 2020 03:14:13: start model_add_line... INFO @ Tue, 30 Jun 2020 03:14:13: start X-correlation... INFO @ Tue, 30 Jun 2020 03:14:13: end of X-cor INFO @ Tue, 30 Jun 2020 03:14:13: #2 finished! INFO @ Tue, 30 Jun 2020 03:14:13: #2 predicted fragment length is 57 bps INFO @ Tue, 30 Jun 2020 03:14:13: #2 alternative fragment length(s) may be 31,57,87,127,155,255,285,316,383,451,472,482,549 bps INFO @ Tue, 30 Jun 2020 03:14:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.05_model.r WARNING @ Tue, 30 Jun 2020 03:14:13: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:14:13: #2 You may need to consider one of the other alternative d(s): 31,57,87,127,155,255,285,316,383,451,472,482,549 WARNING @ Tue, 30 Jun 2020 03:14:13: #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 03:14:13: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:14:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:14:14: 11000000 INFO @ Tue, 30 Jun 2020 03:14:17: 8000000 INFO @ Tue, 30 Jun 2020 03:14:20: 12000000 INFO @ Tue, 30 Jun 2020 03:14:23: 9000000 INFO @ Tue, 30 Jun 2020 03:14:27: 13000000 INFO @ Tue, 30 Jun 2020 03:14:29: 10000000 INFO @ Tue, 30 Jun 2020 03:14:33: 14000000 INFO @ Tue, 30 Jun 2020 03:14:35: 11000000 INFO @ Tue, 30 Jun 2020 03:14:40: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:14:40: 15000000 INFO @ Tue, 30 Jun 2020 03:14:41: 12000000 INFO @ Tue, 30 Jun 2020 03:14:42: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:14:42: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:14:42: #1 total tags in treatment: 15293323 INFO @ Tue, 30 Jun 2020 03:14:42: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:14:42: #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 03:14:43: #1 tags after filtering in treatment: 15293322 INFO @ Tue, 30 Jun 2020 03:14:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:14:43: #1 finished! INFO @ Tue, 30 Jun 2020 03:14:43: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:14:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:14:44: #2 number of paired peaks: 139 WARNING @ Tue, 30 Jun 2020 03:14:44: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Tue, 30 Jun 2020 03:14:44: start model_add_line... INFO @ Tue, 30 Jun 2020 03:14:44: start X-correlation... INFO @ Tue, 30 Jun 2020 03:14:44: end of X-cor INFO @ Tue, 30 Jun 2020 03:14:44: #2 finished! INFO @ Tue, 30 Jun 2020 03:14:44: #2 predicted fragment length is 57 bps INFO @ Tue, 30 Jun 2020 03:14:44: #2 alternative fragment length(s) may be 31,57,87,127,155,255,285,316,383,451,472,482,549 bps INFO @ Tue, 30 Jun 2020 03:14:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.10_model.r WARNING @ Tue, 30 Jun 2020 03:14:44: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:14:44: #2 You may need to consider one of the other alternative d(s): 31,57,87,127,155,255,285,316,383,451,472,482,549 WARNING @ Tue, 30 Jun 2020 03:14:44: #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 03:14:44: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:14:44: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:14:48: 13000000 INFO @ Tue, 30 Jun 2020 03:14:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:14:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:14:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.05_summits.bed INFO @ Tue, 30 Jun 2020 03:14:54: Done! pass1 - making usageList (260 chroms): 2 millis pass2 - checking and writing primary data (656 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:14:55: 14000000 INFO @ Tue, 30 Jun 2020 03:15:01: 15000000 INFO @ Tue, 30 Jun 2020 03:15:03: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 03:15:03: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 03:15:03: #1 total tags in treatment: 15293323 INFO @ Tue, 30 Jun 2020 03:15:03: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:15:03: #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 03:15:04: #1 tags after filtering in treatment: 15293322 INFO @ Tue, 30 Jun 2020 03:15:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:15:04: #1 finished! INFO @ Tue, 30 Jun 2020 03:15:04: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:15:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:15:05: #2 number of paired peaks: 139 WARNING @ Tue, 30 Jun 2020 03:15:05: Fewer paired peaks (139) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 139 pairs to build model! INFO @ Tue, 30 Jun 2020 03:15:05: start model_add_line... INFO @ Tue, 30 Jun 2020 03:15:05: start X-correlation... INFO @ Tue, 30 Jun 2020 03:15:05: end of X-cor INFO @ Tue, 30 Jun 2020 03:15:05: #2 finished! INFO @ Tue, 30 Jun 2020 03:15:05: #2 predicted fragment length is 57 bps INFO @ Tue, 30 Jun 2020 03:15:05: #2 alternative fragment length(s) may be 31,57,87,127,155,255,285,316,383,451,472,482,549 bps INFO @ Tue, 30 Jun 2020 03:15:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.20_model.r WARNING @ Tue, 30 Jun 2020 03:15:05: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:15:05: #2 You may need to consider one of the other alternative d(s): 31,57,87,127,155,255,285,316,383,451,472,482,549 WARNING @ Tue, 30 Jun 2020 03:15:05: #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 03:15:05: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:15:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:15:10: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:15:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:15:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:15:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.10_summits.bed INFO @ Tue, 30 Jun 2020 03:15:24: Done! pass1 - making usageList (115 chroms): 1 millis pass2 - checking and writing primary data (270 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:15:31: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:15:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:15:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:15:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6468492/SRX6468492.20_summits.bed INFO @ Tue, 30 Jun 2020 03:15:45: Done! pass1 - making usageList (68 chroms): 1 millis pass2 - checking and writing primary data (121 records, 4 fields): 5 millis CompletedMACS2peakCalling