Job ID = 6529359 SRX = SRX202834 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: 00:04:24 12145465 reads; of these: 12145465 (100.00%) were unpaired; of these: 340646 (2.80%) aligned 0 times 9574753 (78.83%) aligned exactly 1 time 2230066 (18.36%) aligned >1 times 97.20% overall alignment rate Time searching: 00:04:24 Overall time: 00:04:24 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] 1645166 / 11804819 = 0.1394 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 01:51:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.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 01:51:47: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:51:47: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:51:53: 1000000 INFO @ Tue, 30 Jun 2020 01:51:59: 2000000 INFO @ Tue, 30 Jun 2020 01:52:05: 3000000 INFO @ Tue, 30 Jun 2020 01:52:11: 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 01:52:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.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 01:52:17: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:52:17: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:52:18: 5000000 INFO @ Tue, 30 Jun 2020 01:52:24: 1000000 INFO @ Tue, 30 Jun 2020 01:52:25: 6000000 INFO @ Tue, 30 Jun 2020 01:52:31: 2000000 INFO @ Tue, 30 Jun 2020 01:52:32: 7000000 INFO @ Tue, 30 Jun 2020 01:52:38: 3000000 INFO @ Tue, 30 Jun 2020 01:52:39: 8000000 INFO @ Tue, 30 Jun 2020 01:52:45: 4000000 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 01:52:46: 9000000 INFO @ Tue, 30 Jun 2020 01:52:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.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 01:52:47: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:52:47: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:52:52: 5000000 INFO @ Tue, 30 Jun 2020 01:52:54: 10000000 INFO @ Tue, 30 Jun 2020 01:52:55: 1000000 INFO @ Tue, 30 Jun 2020 01:52:55: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 01:52:55: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 01:52:55: #1 total tags in treatment: 10159653 INFO @ Tue, 30 Jun 2020 01:52:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:52:55: #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 01:52:56: #1 tags after filtering in treatment: 10159649 INFO @ Tue, 30 Jun 2020 01:52:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:52:56: #1 finished! INFO @ Tue, 30 Jun 2020 01:52:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:52:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:52:56: #2 number of paired peaks: 158 WARNING @ Tue, 30 Jun 2020 01:52:56: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 30 Jun 2020 01:52:56: start model_add_line... INFO @ Tue, 30 Jun 2020 01:52:56: start X-correlation... INFO @ Tue, 30 Jun 2020 01:52:56: end of X-cor INFO @ Tue, 30 Jun 2020 01:52:56: #2 finished! INFO @ Tue, 30 Jun 2020 01:52:56: #2 predicted fragment length is 70 bps INFO @ Tue, 30 Jun 2020 01:52:56: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 30 Jun 2020 01:52:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.05_model.r WARNING @ Tue, 30 Jun 2020 01:52:56: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:52:56: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 30 Jun 2020 01:52:56: #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 01:52:56: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:52:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:53:00: 6000000 INFO @ Tue, 30 Jun 2020 01:53:04: 2000000 INFO @ Tue, 30 Jun 2020 01:53:08: 7000000 INFO @ Tue, 30 Jun 2020 01:53:12: 3000000 INFO @ Tue, 30 Jun 2020 01:53:15: 8000000 INFO @ Tue, 30 Jun 2020 01:53:17: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:53:20: 4000000 INFO @ Tue, 30 Jun 2020 01:53:23: 9000000 INFO @ Tue, 30 Jun 2020 01:53:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:53:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:53:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.05_summits.bed INFO @ Tue, 30 Jun 2020 01:53:27: Done! pass1 - making usageList (222 chroms): 1 millis pass2 - checking and writing primary data (493 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:53:29: 5000000 INFO @ Tue, 30 Jun 2020 01:53:30: 10000000 INFO @ Tue, 30 Jun 2020 01:53:32: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 01:53:32: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 01:53:32: #1 total tags in treatment: 10159653 INFO @ Tue, 30 Jun 2020 01:53:32: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:53:32: #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 01:53:32: #1 tags after filtering in treatment: 10159649 INFO @ Tue, 30 Jun 2020 01:53:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:53:32: #1 finished! INFO @ Tue, 30 Jun 2020 01:53:32: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:53:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:53:33: #2 number of paired peaks: 158 WARNING @ Tue, 30 Jun 2020 01:53:33: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 30 Jun 2020 01:53:33: start model_add_line... INFO @ Tue, 30 Jun 2020 01:53:33: start X-correlation... INFO @ Tue, 30 Jun 2020 01:53:33: end of X-cor INFO @ Tue, 30 Jun 2020 01:53:33: #2 finished! INFO @ Tue, 30 Jun 2020 01:53:33: #2 predicted fragment length is 70 bps INFO @ Tue, 30 Jun 2020 01:53:33: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 30 Jun 2020 01:53:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.10_model.r WARNING @ Tue, 30 Jun 2020 01:53:33: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:53:33: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 30 Jun 2020 01:53:33: #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 01:53:33: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:53:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:53:37: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:53:45: 7000000 INFO @ Tue, 30 Jun 2020 01:53:53: 8000000 INFO @ Tue, 30 Jun 2020 01:53:53: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:54:01: 9000000 INFO @ Tue, 30 Jun 2020 01:54:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:54:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:54:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.10_summits.bed INFO @ Tue, 30 Jun 2020 01:54:04: Done! BigWig に変換しました。 pass1 - making usageList (137 chroms): 1 millis pass2 - checking and writing primary data (307 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 01:54:08: 10000000 INFO @ Tue, 30 Jun 2020 01:54:10: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 01:54:10: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 01:54:10: #1 total tags in treatment: 10159653 INFO @ Tue, 30 Jun 2020 01:54:10: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:54:10: #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 01:54:10: #1 tags after filtering in treatment: 10159649 INFO @ Tue, 30 Jun 2020 01:54:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:54:10: #1 finished! INFO @ Tue, 30 Jun 2020 01:54:10: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:54:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:54:11: #2 number of paired peaks: 158 WARNING @ Tue, 30 Jun 2020 01:54:11: Fewer paired peaks (158) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 158 pairs to build model! INFO @ Tue, 30 Jun 2020 01:54:11: start model_add_line... INFO @ Tue, 30 Jun 2020 01:54:11: start X-correlation... INFO @ Tue, 30 Jun 2020 01:54:11: end of X-cor INFO @ Tue, 30 Jun 2020 01:54:11: #2 finished! INFO @ Tue, 30 Jun 2020 01:54:11: #2 predicted fragment length is 70 bps INFO @ Tue, 30 Jun 2020 01:54:11: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 30 Jun 2020 01:54:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.20_model.r WARNING @ Tue, 30 Jun 2020 01:54:11: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:54:11: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 30 Jun 2020 01:54:11: #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 01:54:11: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:54:11: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:54:31: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:54:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:54:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:54:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX202834/SRX202834.20_summits.bed INFO @ Tue, 30 Jun 2020 01:54:41: Done! pass1 - making usageList (111 chroms): 1 millis pass2 - checking and writing primary data (218 records, 4 fields): 5 millis CompletedMACS2peakCalling