Job ID = 6529824 SRX = SRX495209 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: 00:04:33 17232507 reads; of these: 17232507 (100.00%) were unpaired; of these: 337984 (1.96%) aligned 0 times 12616970 (73.22%) aligned exactly 1 time 4277553 (24.82%) aligned >1 times 98.04% overall alignment rate Time searching: 00:04:33 Overall time: 00:04:33 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] 3805002 / 16894523 = 0.2252 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 03:28:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.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 03:28:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:28:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:28:26: 1000000 INFO @ Tue, 30 Jun 2020 03:28:32: 2000000 INFO @ Tue, 30 Jun 2020 03:28:38: 3000000 INFO @ Tue, 30 Jun 2020 03:28:44: 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 03:28:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.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 03:28:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:28:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:28:50: 5000000 INFO @ Tue, 30 Jun 2020 03:28:56: 1000000 INFO @ Tue, 30 Jun 2020 03:28:57: 6000000 INFO @ Tue, 30 Jun 2020 03:29:02: 2000000 INFO @ Tue, 30 Jun 2020 03:29:04: 7000000 INFO @ Tue, 30 Jun 2020 03:29:09: 3000000 INFO @ Tue, 30 Jun 2020 03:29:10: 8000000 INFO @ Tue, 30 Jun 2020 03:29:15: 4000000 INFO @ Tue, 30 Jun 2020 03:29:17: 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 03:29:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.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 03:29:19: #1 read tag files... INFO @ Tue, 30 Jun 2020 03:29:19: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 03:29:22: 5000000 INFO @ Tue, 30 Jun 2020 03:29:24: 10000000 INFO @ Tue, 30 Jun 2020 03:29:26: 1000000 INFO @ Tue, 30 Jun 2020 03:29:29: 6000000 INFO @ Tue, 30 Jun 2020 03:29:31: 11000000 INFO @ Tue, 30 Jun 2020 03:29:32: 2000000 INFO @ Tue, 30 Jun 2020 03:29:36: 7000000 INFO @ Tue, 30 Jun 2020 03:29:38: 3000000 INFO @ Tue, 30 Jun 2020 03:29:38: 12000000 INFO @ Tue, 30 Jun 2020 03:29:42: 8000000 INFO @ Tue, 30 Jun 2020 03:29:44: 4000000 INFO @ Tue, 30 Jun 2020 03:29:45: 13000000 INFO @ Tue, 30 Jun 2020 03:29:46: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 03:29:46: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 03:29:46: #1 total tags in treatment: 13089521 INFO @ Tue, 30 Jun 2020 03:29:46: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:29:46: #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 03:29:46: #1 tags after filtering in treatment: 13089521 INFO @ Tue, 30 Jun 2020 03:29:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:29:46: #1 finished! INFO @ Tue, 30 Jun 2020 03:29:46: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:29:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:29:47: #2 number of paired peaks: 127 WARNING @ Tue, 30 Jun 2020 03:29:47: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Tue, 30 Jun 2020 03:29:47: start model_add_line... INFO @ Tue, 30 Jun 2020 03:29:47: start X-correlation... INFO @ Tue, 30 Jun 2020 03:29:47: end of X-cor INFO @ Tue, 30 Jun 2020 03:29:47: #2 finished! INFO @ Tue, 30 Jun 2020 03:29:47: #2 predicted fragment length is 69 bps INFO @ Tue, 30 Jun 2020 03:29:47: #2 alternative fragment length(s) may be 4,20,46,69,527,535,537,569,591 bps INFO @ Tue, 30 Jun 2020 03:29:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.05_model.r WARNING @ Tue, 30 Jun 2020 03:29:47: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:29:47: #2 You may need to consider one of the other alternative d(s): 4,20,46,69,527,535,537,569,591 WARNING @ Tue, 30 Jun 2020 03:29:47: #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 03:29:47: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:29:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:29:49: 9000000 INFO @ Tue, 30 Jun 2020 03:29:50: 5000000 INFO @ Tue, 30 Jun 2020 03:29:56: 10000000 INFO @ Tue, 30 Jun 2020 03:29:56: 6000000 INFO @ Tue, 30 Jun 2020 03:30:02: 7000000 INFO @ Tue, 30 Jun 2020 03:30:03: 11000000 INFO @ Tue, 30 Jun 2020 03:30:08: 8000000 INFO @ Tue, 30 Jun 2020 03:30:09: 12000000 INFO @ Tue, 30 Jun 2020 03:30:12: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:30:14: 9000000 INFO @ Tue, 30 Jun 2020 03:30:16: 13000000 INFO @ Tue, 30 Jun 2020 03:30:17: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 03:30:17: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 03:30:17: #1 total tags in treatment: 13089521 INFO @ Tue, 30 Jun 2020 03:30:17: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:30:17: #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 03:30:17: #1 tags after filtering in treatment: 13089521 INFO @ Tue, 30 Jun 2020 03:30:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:30:17: #1 finished! INFO @ Tue, 30 Jun 2020 03:30:17: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:30:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:30:18: #2 number of paired peaks: 127 WARNING @ Tue, 30 Jun 2020 03:30:18: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Tue, 30 Jun 2020 03:30:18: start model_add_line... INFO @ Tue, 30 Jun 2020 03:30:18: start X-correlation... INFO @ Tue, 30 Jun 2020 03:30:18: end of X-cor INFO @ Tue, 30 Jun 2020 03:30:18: #2 finished! INFO @ Tue, 30 Jun 2020 03:30:18: #2 predicted fragment length is 69 bps INFO @ Tue, 30 Jun 2020 03:30:18: #2 alternative fragment length(s) may be 4,20,46,69,527,535,537,569,591 bps INFO @ Tue, 30 Jun 2020 03:30:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.10_model.r WARNING @ Tue, 30 Jun 2020 03:30:18: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:30:18: #2 You may need to consider one of the other alternative d(s): 4,20,46,69,527,535,537,569,591 WARNING @ Tue, 30 Jun 2020 03:30:18: #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 03:30:18: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:30:18: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:30:20: 10000000 INFO @ Tue, 30 Jun 2020 03:30:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:30:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:30:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.05_summits.bed INFO @ Tue, 30 Jun 2020 03:30:25: Done! pass1 - making usageList (348 chroms): 1 millis pass2 - checking and writing primary data (715 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:30:26: 11000000 INFO @ Tue, 30 Jun 2020 03:30:31: 12000000 INFO @ Tue, 30 Jun 2020 03:30:37: 13000000 INFO @ Tue, 30 Jun 2020 03:30:37: #1 tag size is determined as 44 bps INFO @ Tue, 30 Jun 2020 03:30:37: #1 tag size = 44 INFO @ Tue, 30 Jun 2020 03:30:37: #1 total tags in treatment: 13089521 INFO @ Tue, 30 Jun 2020 03:30:37: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:30:37: #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 03:30:38: #1 tags after filtering in treatment: 13089521 INFO @ Tue, 30 Jun 2020 03:30:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:30:38: #1 finished! INFO @ Tue, 30 Jun 2020 03:30:38: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:30:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:30:39: #2 number of paired peaks: 127 WARNING @ Tue, 30 Jun 2020 03:30:39: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Tue, 30 Jun 2020 03:30:39: start model_add_line... INFO @ Tue, 30 Jun 2020 03:30:39: start X-correlation... INFO @ Tue, 30 Jun 2020 03:30:39: end of X-cor INFO @ Tue, 30 Jun 2020 03:30:39: #2 finished! INFO @ Tue, 30 Jun 2020 03:30:39: #2 predicted fragment length is 69 bps INFO @ Tue, 30 Jun 2020 03:30:39: #2 alternative fragment length(s) may be 4,20,46,69,527,535,537,569,591 bps INFO @ Tue, 30 Jun 2020 03:30:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.20_model.r WARNING @ Tue, 30 Jun 2020 03:30:39: #2 Since the d (69) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 03:30:39: #2 You may need to consider one of the other alternative d(s): 4,20,46,69,527,535,537,569,591 WARNING @ Tue, 30 Jun 2020 03:30:39: #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 03:30:39: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:30:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:30:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:30:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:30:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:30:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.10_summits.bed INFO @ Tue, 30 Jun 2020 03:30:55: Done! pass1 - making usageList (109 chroms): 1 millis pass2 - checking and writing primary data (246 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:31:04: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:31:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:31:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:31:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX495209/SRX495209.20_summits.bed INFO @ Tue, 30 Jun 2020 03:31:17: Done! pass1 - making usageList (75 chroms): 1 millis pass2 - checking and writing primary data (144 records, 4 fields): 3 millis CompletedMACS2peakCalling