Job ID = 6529281 SRX = SRX1167621 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: 00:05:07 23931965 reads; of these: 23931965 (100.00%) were unpaired; of these: 512545 (2.14%) aligned 0 times 18704616 (78.16%) aligned exactly 1 time 4714804 (19.70%) aligned >1 times 97.86% overall alignment rate Time searching: 00:05:07 Overall time: 00:05:07 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] 8071845 / 23419420 = 0.3447 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 01:46:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.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 01:46:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:46:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:47:00: 1000000 INFO @ Tue, 30 Jun 2020 01:47:06: 2000000 INFO @ Tue, 30 Jun 2020 01:47:11: 3000000 INFO @ Tue, 30 Jun 2020 01:47:17: 4000000 INFO @ Tue, 30 Jun 2020 01:47:22: 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 01:47:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.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 01:47:25: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:47:25: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:47:28: 6000000 INFO @ Tue, 30 Jun 2020 01:47:30: 1000000 INFO @ Tue, 30 Jun 2020 01:47:34: 7000000 INFO @ Tue, 30 Jun 2020 01:47:35: 2000000 INFO @ Tue, 30 Jun 2020 01:47:40: 8000000 INFO @ Tue, 30 Jun 2020 01:47:40: 3000000 INFO @ Tue, 30 Jun 2020 01:47:45: 4000000 INFO @ Tue, 30 Jun 2020 01:47:45: 9000000 INFO @ Tue, 30 Jun 2020 01:47:50: 5000000 INFO @ Tue, 30 Jun 2020 01:47:51: 10000000 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 01:47:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.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 01:47:55: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:47:55: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:47:56: 6000000 INFO @ Tue, 30 Jun 2020 01:47:57: 11000000 INFO @ Tue, 30 Jun 2020 01:48:00: 1000000 INFO @ Tue, 30 Jun 2020 01:48:01: 7000000 INFO @ Tue, 30 Jun 2020 01:48:02: 12000000 INFO @ Tue, 30 Jun 2020 01:48:06: 2000000 INFO @ Tue, 30 Jun 2020 01:48:06: 8000000 INFO @ Tue, 30 Jun 2020 01:48:08: 13000000 INFO @ Tue, 30 Jun 2020 01:48:11: 9000000 INFO @ Tue, 30 Jun 2020 01:48:12: 3000000 INFO @ Tue, 30 Jun 2020 01:48:14: 14000000 INFO @ Tue, 30 Jun 2020 01:48:16: 10000000 INFO @ Tue, 30 Jun 2020 01:48:17: 4000000 INFO @ Tue, 30 Jun 2020 01:48:20: 15000000 INFO @ Tue, 30 Jun 2020 01:48:21: 11000000 INFO @ Tue, 30 Jun 2020 01:48:22: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:48:22: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:48:22: #1 total tags in treatment: 15347575 INFO @ Tue, 30 Jun 2020 01:48:22: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:48:22: #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 01:48:22: #1 tags after filtering in treatment: 15347479 INFO @ Tue, 30 Jun 2020 01:48:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:48:22: #1 finished! INFO @ Tue, 30 Jun 2020 01:48:22: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:48:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:48:23: 5000000 INFO @ Tue, 30 Jun 2020 01:48:23: #2 number of paired peaks: 343 WARNING @ Tue, 30 Jun 2020 01:48:23: Fewer paired peaks (343) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 343 pairs to build model! INFO @ Tue, 30 Jun 2020 01:48:23: start model_add_line... INFO @ Tue, 30 Jun 2020 01:48:23: start X-correlation... INFO @ Tue, 30 Jun 2020 01:48:23: end of X-cor INFO @ Tue, 30 Jun 2020 01:48:23: #2 finished! INFO @ Tue, 30 Jun 2020 01:48:23: #2 predicted fragment length is 55 bps INFO @ Tue, 30 Jun 2020 01:48:23: #2 alternative fragment length(s) may be 4,55 bps INFO @ Tue, 30 Jun 2020 01:48:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.05_model.r WARNING @ Tue, 30 Jun 2020 01:48:23: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:48:23: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Tue, 30 Jun 2020 01:48:23: #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 01:48:23: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:48:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:48:27: 12000000 INFO @ Tue, 30 Jun 2020 01:48:29: 6000000 INFO @ Tue, 30 Jun 2020 01:48:32: 13000000 INFO @ Tue, 30 Jun 2020 01:48:34: 7000000 INFO @ Tue, 30 Jun 2020 01:48:37: 14000000 INFO @ Tue, 30 Jun 2020 01:48:40: 8000000 INFO @ Tue, 30 Jun 2020 01:48:42: 15000000 INFO @ Tue, 30 Jun 2020 01:48:44: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:48:44: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:48:44: #1 total tags in treatment: 15347575 INFO @ Tue, 30 Jun 2020 01:48:44: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:48:44: #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 01:48:45: #1 tags after filtering in treatment: 15347479 INFO @ Tue, 30 Jun 2020 01:48:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:48:45: #1 finished! INFO @ Tue, 30 Jun 2020 01:48:45: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:48:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:48:46: 9000000 INFO @ Tue, 30 Jun 2020 01:48:46: #2 number of paired peaks: 343 WARNING @ Tue, 30 Jun 2020 01:48:46: Fewer paired peaks (343) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 343 pairs to build model! INFO @ Tue, 30 Jun 2020 01:48:46: start model_add_line... INFO @ Tue, 30 Jun 2020 01:48:46: start X-correlation... INFO @ Tue, 30 Jun 2020 01:48:46: end of X-cor INFO @ Tue, 30 Jun 2020 01:48:46: #2 finished! INFO @ Tue, 30 Jun 2020 01:48:46: #2 predicted fragment length is 55 bps INFO @ Tue, 30 Jun 2020 01:48:46: #2 alternative fragment length(s) may be 4,55 bps INFO @ Tue, 30 Jun 2020 01:48:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.10_model.r WARNING @ Tue, 30 Jun 2020 01:48:46: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:48:46: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Tue, 30 Jun 2020 01:48:46: #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 01:48:46: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:48:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:48:51: 10000000 INFO @ Tue, 30 Jun 2020 01:48:52: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:48:57: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:49:02: 12000000 INFO @ Tue, 30 Jun 2020 01:49:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:49:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:49:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.05_summits.bed INFO @ Tue, 30 Jun 2020 01:49:06: Done! pass1 - making usageList (469 chroms): 1 millis pass2 - checking and writing primary data (1840 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:49:08: 13000000 INFO @ Tue, 30 Jun 2020 01:49:13: 14000000 INFO @ Tue, 30 Jun 2020 01:49:15: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:49:18: 15000000 INFO @ Tue, 30 Jun 2020 01:49:21: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 01:49:21: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 01:49:21: #1 total tags in treatment: 15347575 INFO @ Tue, 30 Jun 2020 01:49:21: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:49:21: #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 01:49:21: #1 tags after filtering in treatment: 15347479 INFO @ Tue, 30 Jun 2020 01:49:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:49:21: #1 finished! INFO @ Tue, 30 Jun 2020 01:49:21: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:49:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:49:22: #2 number of paired peaks: 343 WARNING @ Tue, 30 Jun 2020 01:49:22: Fewer paired peaks (343) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 343 pairs to build model! INFO @ Tue, 30 Jun 2020 01:49:22: start model_add_line... INFO @ Tue, 30 Jun 2020 01:49:22: start X-correlation... INFO @ Tue, 30 Jun 2020 01:49:22: end of X-cor INFO @ Tue, 30 Jun 2020 01:49:22: #2 finished! INFO @ Tue, 30 Jun 2020 01:49:22: #2 predicted fragment length is 55 bps INFO @ Tue, 30 Jun 2020 01:49:22: #2 alternative fragment length(s) may be 4,55 bps INFO @ Tue, 30 Jun 2020 01:49:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.20_model.r WARNING @ Tue, 30 Jun 2020 01:49:22: #2 Since the d (55) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:49:22: #2 You may need to consider one of the other alternative d(s): 4,55 WARNING @ Tue, 30 Jun 2020 01:49:22: #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 01:49:22: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:49:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:49:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:49:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:49:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.10_summits.bed INFO @ Tue, 30 Jun 2020 01:49:29: Done! pass1 - making usageList (280 chroms): 1 millis pass2 - checking and writing primary data (753 records, 4 fields): 8 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:49:52: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:50:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:50:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:50:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1167621/SRX1167621.20_summits.bed INFO @ Tue, 30 Jun 2020 01:50:06: Done! pass1 - making usageList (115 chroms): 1 millis pass2 - checking and writing primary data (310 records, 4 fields): 4 millis CompletedMACS2peakCalling