Job ID = 6529245 SRX = SRX110788 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: 00:05:28 16261620 reads; of these: 16261620 (100.00%) were unpaired; of these: 383444 (2.36%) aligned 0 times 7821246 (48.10%) aligned exactly 1 time 8056930 (49.55%) aligned >1 times 97.64% overall alignment rate Time searching: 00:05:28 Overall time: 00:05:28 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_rmdupse_core] 1389571 / 15878176 = 0.0875 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 01:40:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.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 01:40:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:40:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:40:26: 1000000 INFO @ Tue, 30 Jun 2020 01:40:31: 2000000 INFO @ Tue, 30 Jun 2020 01:40:37: 3000000 INFO @ Tue, 30 Jun 2020 01:40:42: 4000000 INFO @ Tue, 30 Jun 2020 01:40:48: 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 01:40:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.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 01:40:50: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:40:50: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:40:53: 6000000 INFO @ Tue, 30 Jun 2020 01:40:56: 1000000 INFO @ Tue, 30 Jun 2020 01:40:59: 7000000 INFO @ Tue, 30 Jun 2020 01:41:02: 2000000 INFO @ Tue, 30 Jun 2020 01:41:05: 8000000 INFO @ Tue, 30 Jun 2020 01:41:07: 3000000 INFO @ Tue, 30 Jun 2020 01:41:10: 9000000 INFO @ Tue, 30 Jun 2020 01:41:13: 4000000 INFO @ Tue, 30 Jun 2020 01:41:16: 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 01:41:19: 5000000 INFO @ Tue, 30 Jun 2020 01:41:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.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 01:41:20: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:41:20: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:41:22: 11000000 INFO @ Tue, 30 Jun 2020 01:41:24: 6000000 INFO @ Tue, 30 Jun 2020 01:41:26: 1000000 INFO @ Tue, 30 Jun 2020 01:41:28: 12000000 INFO @ Tue, 30 Jun 2020 01:41:30: 7000000 INFO @ Tue, 30 Jun 2020 01:41:32: 2000000 INFO @ Tue, 30 Jun 2020 01:41:34: 13000000 INFO @ Tue, 30 Jun 2020 01:41:36: 8000000 INFO @ Tue, 30 Jun 2020 01:41:38: 3000000 INFO @ Tue, 30 Jun 2020 01:41:40: 14000000 INFO @ Tue, 30 Jun 2020 01:41:42: 9000000 INFO @ Tue, 30 Jun 2020 01:41:43: #1 tag size is determined as 18 bps INFO @ Tue, 30 Jun 2020 01:41:43: #1 tag size = 18 INFO @ Tue, 30 Jun 2020 01:41:43: #1 total tags in treatment: 14488605 INFO @ Tue, 30 Jun 2020 01:41:43: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:41:43: #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 01:41:44: 4000000 INFO @ Tue, 30 Jun 2020 01:41:44: #1 tags after filtering in treatment: 14488605 INFO @ Tue, 30 Jun 2020 01:41:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:41:44: #1 finished! INFO @ Tue, 30 Jun 2020 01:41:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:41:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:41:45: #2 number of paired peaks: 298 WARNING @ Tue, 30 Jun 2020 01:41:45: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Tue, 30 Jun 2020 01:41:45: start model_add_line... INFO @ Tue, 30 Jun 2020 01:41:45: start X-correlation... INFO @ Tue, 30 Jun 2020 01:41:45: end of X-cor INFO @ Tue, 30 Jun 2020 01:41:45: #2 finished! INFO @ Tue, 30 Jun 2020 01:41:45: #2 predicted fragment length is 18 bps INFO @ Tue, 30 Jun 2020 01:41:45: #2 alternative fragment length(s) may be 3,18 bps INFO @ Tue, 30 Jun 2020 01:41:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.05_model.r WARNING @ Tue, 30 Jun 2020 01:41:45: #2 Since the d (18) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:41:45: #2 You may need to consider one of the other alternative d(s): 3,18 WARNING @ Tue, 30 Jun 2020 01:41:45: #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 01:41:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:41:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:41:48: 10000000 INFO @ Tue, 30 Jun 2020 01:41:50: 5000000 INFO @ Tue, 30 Jun 2020 01:41:53: 11000000 INFO @ Tue, 30 Jun 2020 01:41:55: 6000000 INFO @ Tue, 30 Jun 2020 01:42:00: 12000000 INFO @ Tue, 30 Jun 2020 01:42:01: 7000000 INFO @ Tue, 30 Jun 2020 01:42:06: 13000000 INFO @ Tue, 30 Jun 2020 01:42:07: 8000000 INFO @ Tue, 30 Jun 2020 01:42:11: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:42:11: 14000000 INFO @ Tue, 30 Jun 2020 01:42:12: 9000000 INFO @ Tue, 30 Jun 2020 01:42:15: #1 tag size is determined as 18 bps INFO @ Tue, 30 Jun 2020 01:42:15: #1 tag size = 18 INFO @ Tue, 30 Jun 2020 01:42:15: #1 total tags in treatment: 14488605 INFO @ Tue, 30 Jun 2020 01:42:15: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:42:15: #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 01:42:15: #1 tags after filtering in treatment: 14488605 INFO @ Tue, 30 Jun 2020 01:42:15: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:42:15: #1 finished! INFO @ Tue, 30 Jun 2020 01:42:15: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:42:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:42:16: #2 number of paired peaks: 298 WARNING @ Tue, 30 Jun 2020 01:42:16: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Tue, 30 Jun 2020 01:42:16: start model_add_line... INFO @ Tue, 30 Jun 2020 01:42:16: start X-correlation... INFO @ Tue, 30 Jun 2020 01:42:16: end of X-cor INFO @ Tue, 30 Jun 2020 01:42:16: #2 finished! INFO @ Tue, 30 Jun 2020 01:42:16: #2 predicted fragment length is 18 bps INFO @ Tue, 30 Jun 2020 01:42:16: #2 alternative fragment length(s) may be 3,18 bps INFO @ Tue, 30 Jun 2020 01:42:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.10_model.r WARNING @ Tue, 30 Jun 2020 01:42:16: #2 Since the d (18) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:42:16: #2 You may need to consider one of the other alternative d(s): 3,18 WARNING @ Tue, 30 Jun 2020 01:42:16: #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 01:42:16: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:42:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:42:18: 10000000 INFO @ Tue, 30 Jun 2020 01:42:23: 11000000 INFO @ Tue, 30 Jun 2020 01:42:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:42:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:42:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.05_summits.bed INFO @ Tue, 30 Jun 2020 01:42:25: Done! pass1 - making usageList (275 chroms): 2 millis pass2 - checking and writing primary data (800 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:42:30: 12000000 INFO @ Tue, 30 Jun 2020 01:42:35: 13000000 INFO @ Tue, 30 Jun 2020 01:42:40: 14000000 INFO @ Tue, 30 Jun 2020 01:42:42: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:42:43: #1 tag size is determined as 18 bps INFO @ Tue, 30 Jun 2020 01:42:43: #1 tag size = 18 INFO @ Tue, 30 Jun 2020 01:42:43: #1 total tags in treatment: 14488605 INFO @ Tue, 30 Jun 2020 01:42:43: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:42:43: #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 01:42:44: #1 tags after filtering in treatment: 14488605 INFO @ Tue, 30 Jun 2020 01:42:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:42:44: #1 finished! INFO @ Tue, 30 Jun 2020 01:42:44: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:42:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:42:45: #2 number of paired peaks: 298 WARNING @ Tue, 30 Jun 2020 01:42:45: Fewer paired peaks (298) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 298 pairs to build model! INFO @ Tue, 30 Jun 2020 01:42:45: start model_add_line... INFO @ Tue, 30 Jun 2020 01:42:45: start X-correlation... INFO @ Tue, 30 Jun 2020 01:42:45: end of X-cor INFO @ Tue, 30 Jun 2020 01:42:45: #2 finished! INFO @ Tue, 30 Jun 2020 01:42:45: #2 predicted fragment length is 18 bps INFO @ Tue, 30 Jun 2020 01:42:45: #2 alternative fragment length(s) may be 3,18 bps INFO @ Tue, 30 Jun 2020 01:42:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.20_model.r WARNING @ Tue, 30 Jun 2020 01:42:45: #2 Since the d (18) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:42:45: #2 You may need to consider one of the other alternative d(s): 3,18 WARNING @ Tue, 30 Jun 2020 01:42:45: #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 01:42:45: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:42:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:42:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:42:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:42:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.10_summits.bed INFO @ Tue, 30 Jun 2020 01:42:55: Done! pass1 - making usageList (103 chroms): 1 millis pass2 - checking and writing primary data (326 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:43:10: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:43:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:43:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:43:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX110788/SRX110788.20_summits.bed INFO @ Tue, 30 Jun 2020 01:43:23: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (79 records, 4 fields): 5 millis CompletedMACS2peakCalling