Job ID = 6529532 SRX = SRX287974 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: 00:05:01 17573762 reads; of these: 17573762 (100.00%) were unpaired; of these: 1129164 (6.43%) aligned 0 times 10855788 (61.77%) aligned exactly 1 time 5588810 (31.80%) aligned >1 times 93.57% overall alignment rate Time searching: 00:05:01 Overall time: 00:05:01 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] 2354407 / 16444598 = 0.1432 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 02:26:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.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 02:26:47: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:26:47: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:26:52: 1000000 INFO @ Tue, 30 Jun 2020 02:26:57: 2000000 INFO @ Tue, 30 Jun 2020 02:27:02: 3000000 INFO @ Tue, 30 Jun 2020 02:27:07: 4000000 INFO @ Tue, 30 Jun 2020 02:27:12: 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 02:27:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.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 02:27:17: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:27:17: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:27:17: 6000000 INFO @ Tue, 30 Jun 2020 02:27:22: 1000000 INFO @ Tue, 30 Jun 2020 02:27:23: 7000000 INFO @ Tue, 30 Jun 2020 02:27:28: 2000000 INFO @ Tue, 30 Jun 2020 02:27:28: 8000000 INFO @ Tue, 30 Jun 2020 02:27:33: 3000000 INFO @ Tue, 30 Jun 2020 02:27:33: 9000000 INFO @ Tue, 30 Jun 2020 02:27:38: 4000000 INFO @ Tue, 30 Jun 2020 02:27:38: 10000000 INFO @ Tue, 30 Jun 2020 02:27:43: 5000000 INFO @ Tue, 30 Jun 2020 02:27:44: 11000000 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 02:27:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.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 02:27:47: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:27:47: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:27:49: 6000000 INFO @ Tue, 30 Jun 2020 02:27:49: 12000000 INFO @ Tue, 30 Jun 2020 02:27:52: 1000000 INFO @ Tue, 30 Jun 2020 02:27:54: 7000000 INFO @ Tue, 30 Jun 2020 02:27:55: 13000000 INFO @ Tue, 30 Jun 2020 02:27:58: 2000000 INFO @ Tue, 30 Jun 2020 02:27:59: 8000000 INFO @ Tue, 30 Jun 2020 02:28:00: 14000000 INFO @ Tue, 30 Jun 2020 02:28:01: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:28:01: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:28:01: #1 total tags in treatment: 14090191 INFO @ Tue, 30 Jun 2020 02:28:01: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:28:01: #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 02:28:01: #1 tags after filtering in treatment: 14090191 INFO @ Tue, 30 Jun 2020 02:28:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:28:01: #1 finished! INFO @ Tue, 30 Jun 2020 02:28:01: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:28:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:28:02: #2 number of paired peaks: 692 WARNING @ Tue, 30 Jun 2020 02:28:02: Fewer paired peaks (692) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 692 pairs to build model! INFO @ Tue, 30 Jun 2020 02:28:02: start model_add_line... INFO @ Tue, 30 Jun 2020 02:28:02: start X-correlation... INFO @ Tue, 30 Jun 2020 02:28:02: end of X-cor INFO @ Tue, 30 Jun 2020 02:28:02: #2 finished! INFO @ Tue, 30 Jun 2020 02:28:02: #2 predicted fragment length is 43 bps INFO @ Tue, 30 Jun 2020 02:28:02: #2 alternative fragment length(s) may be 3,43 bps INFO @ Tue, 30 Jun 2020 02:28:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.05_model.r WARNING @ Tue, 30 Jun 2020 02:28:02: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:28:02: #2 You may need to consider one of the other alternative d(s): 3,43 WARNING @ Tue, 30 Jun 2020 02:28:02: #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 02:28:02: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:28:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:28:03: 3000000 INFO @ Tue, 30 Jun 2020 02:28:04: 9000000 INFO @ Tue, 30 Jun 2020 02:28:08: 4000000 INFO @ Tue, 30 Jun 2020 02:28:10: 10000000 INFO @ Tue, 30 Jun 2020 02:28:14: 5000000 INFO @ Tue, 30 Jun 2020 02:28:15: 11000000 INFO @ Tue, 30 Jun 2020 02:28:19: 6000000 INFO @ Tue, 30 Jun 2020 02:28:20: 12000000 INFO @ Tue, 30 Jun 2020 02:28:24: 7000000 INFO @ Tue, 30 Jun 2020 02:28:26: 13000000 INFO @ Tue, 30 Jun 2020 02:28:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:28:29: 8000000 INFO @ Tue, 30 Jun 2020 02:28:31: 14000000 INFO @ Tue, 30 Jun 2020 02:28:32: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:28:32: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:28:32: #1 total tags in treatment: 14090191 INFO @ Tue, 30 Jun 2020 02:28:32: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:28:32: #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 02:28:32: #1 tags after filtering in treatment: 14090191 INFO @ Tue, 30 Jun 2020 02:28:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:28:32: #1 finished! INFO @ Tue, 30 Jun 2020 02:28:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:28:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:28:33: #2 number of paired peaks: 692 WARNING @ Tue, 30 Jun 2020 02:28:33: Fewer paired peaks (692) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 692 pairs to build model! INFO @ Tue, 30 Jun 2020 02:28:33: start model_add_line... INFO @ Tue, 30 Jun 2020 02:28:33: start X-correlation... INFO @ Tue, 30 Jun 2020 02:28:33: end of X-cor INFO @ Tue, 30 Jun 2020 02:28:33: #2 finished! INFO @ Tue, 30 Jun 2020 02:28:33: #2 predicted fragment length is 43 bps INFO @ Tue, 30 Jun 2020 02:28:33: #2 alternative fragment length(s) may be 3,43 bps INFO @ Tue, 30 Jun 2020 02:28:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.10_model.r WARNING @ Tue, 30 Jun 2020 02:28:33: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:28:33: #2 You may need to consider one of the other alternative d(s): 3,43 WARNING @ Tue, 30 Jun 2020 02:28:33: #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 02:28:33: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:28:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:28:34: 9000000 INFO @ Tue, 30 Jun 2020 02:28:40: 10000000 INFO @ Tue, 30 Jun 2020 02:28:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.05_peaks.xls INFO @ Tue, 30 Jun 2020 02:28:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:28:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.05_summits.bed INFO @ Tue, 30 Jun 2020 02:28:43: Done! pass1 - making usageList (747 chroms): 1 millis pass2 - checking and writing primary data (2711 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 02:28:45: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 02:28:50: 12000000 INFO @ Tue, 30 Jun 2020 02:28:55: 13000000 INFO @ Tue, 30 Jun 2020 02:29:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:29:01: 14000000 INFO @ Tue, 30 Jun 2020 02:29:01: #1 tag size is determined as 50 bps INFO @ Tue, 30 Jun 2020 02:29:01: #1 tag size = 50 INFO @ Tue, 30 Jun 2020 02:29:01: #1 total tags in treatment: 14090191 INFO @ Tue, 30 Jun 2020 02:29:01: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:29:01: #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 02:29:02: #1 tags after filtering in treatment: 14090191 INFO @ Tue, 30 Jun 2020 02:29:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:29:02: #1 finished! INFO @ Tue, 30 Jun 2020 02:29:02: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:29:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:29:03: #2 number of paired peaks: 692 WARNING @ Tue, 30 Jun 2020 02:29:03: Fewer paired peaks (692) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 692 pairs to build model! INFO @ Tue, 30 Jun 2020 02:29:03: start model_add_line... INFO @ Tue, 30 Jun 2020 02:29:03: start X-correlation... INFO @ Tue, 30 Jun 2020 02:29:03: end of X-cor INFO @ Tue, 30 Jun 2020 02:29:03: #2 finished! INFO @ Tue, 30 Jun 2020 02:29:03: #2 predicted fragment length is 43 bps INFO @ Tue, 30 Jun 2020 02:29:03: #2 alternative fragment length(s) may be 3,43 bps INFO @ Tue, 30 Jun 2020 02:29:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.20_model.r WARNING @ Tue, 30 Jun 2020 02:29:03: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 02:29:03: #2 You may need to consider one of the other alternative d(s): 3,43 WARNING @ Tue, 30 Jun 2020 02:29:03: #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 02:29:03: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:29:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 02:29:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.10_peaks.xls INFO @ Tue, 30 Jun 2020 02:29:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:29:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.10_summits.bed INFO @ Tue, 30 Jun 2020 02:29:14: Done! pass1 - making usageList (576 chroms): 1 millis pass2 - checking and writing primary data (2104 records, 4 fields): 17 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 02:29:29: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 02:29:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.20_peaks.xls INFO @ Tue, 30 Jun 2020 02:29:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 02:29:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287974/SRX287974.20_summits.bed INFO @ Tue, 30 Jun 2020 02:29:43: Done! pass1 - making usageList (420 chroms): 1 millis pass2 - checking and writing primary data (1048 records, 4 fields): 13 millis CompletedMACS2peakCalling