Job ID = 6627527 SRX = SRX8521345 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: 00:05:25 36474610 reads; of these: 36474610 (100.00%) were unpaired; of these: 31069596 (85.18%) aligned 0 times 4169689 (11.43%) aligned exactly 1 time 1235325 (3.39%) aligned >1 times 14.82% overall alignment rate Time searching: 00:05:25 Overall time: 00:05:25 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] 1067865 / 5405014 = 0.1976 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, 14 Jul 2020 11:57:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.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, 14 Jul 2020 11:57:39: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:57:39: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:57:46: 1000000 INFO @ Tue, 14 Jul 2020 11:57:53: 2000000 INFO @ Tue, 14 Jul 2020 11:57:59: 3000000 INFO @ Tue, 14 Jul 2020 11:58:06: 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, 14 Jul 2020 11:58:08: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 11:58:08: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 11:58:08: #1 total tags in treatment: 4337149 INFO @ Tue, 14 Jul 2020 11:58:08: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:58:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:58:08: #1 tags after filtering in treatment: 4336920 INFO @ Tue, 14 Jul 2020 11:58:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:58:08: #1 finished! INFO @ Tue, 14 Jul 2020 11:58:08: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:58:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:58:09: #2 number of paired peaks: 871 WARNING @ Tue, 14 Jul 2020 11:58:09: Fewer paired peaks (871) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 871 pairs to build model! INFO @ Tue, 14 Jul 2020 11:58:09: start model_add_line... INFO @ Tue, 14 Jul 2020 11:58:09: start X-correlation... INFO @ Tue, 14 Jul 2020 11:58:09: end of X-cor INFO @ Tue, 14 Jul 2020 11:58:09: #2 finished! INFO @ Tue, 14 Jul 2020 11:58:09: #2 predicted fragment length is 69 bps INFO @ Tue, 14 Jul 2020 11:58:09: #2 alternative fragment length(s) may be 69 bps INFO @ Tue, 14 Jul 2020 11:58:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.05_model.r WARNING @ Tue, 14 Jul 2020 11:58:09: #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, 14 Jul 2020 11:58:09: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Tue, 14 Jul 2020 11:58:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:58:09: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:58:09: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:58:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.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, 14 Jul 2020 11:58:09: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:58:09: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:58:16: 1000000 INFO @ Tue, 14 Jul 2020 11:58:19: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:58:22: 2000000 INFO @ Tue, 14 Jul 2020 11:58:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:58:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:58:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.05_summits.bed INFO @ Tue, 14 Jul 2020 11:58:23: Done! pass1 - making usageList (229 chroms): 1 millis pass2 - checking and writing primary data (1101 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:58:29: 3000000 INFO @ Tue, 14 Jul 2020 11:58:36: 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, 14 Jul 2020 11:58:38: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 11:58:38: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 11:58:38: #1 total tags in treatment: 4337149 INFO @ Tue, 14 Jul 2020 11:58:38: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:58:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:58:38: #1 tags after filtering in treatment: 4336920 INFO @ Tue, 14 Jul 2020 11:58:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:58:38: #1 finished! INFO @ Tue, 14 Jul 2020 11:58:38: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:58:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:58:39: #2 number of paired peaks: 871 WARNING @ Tue, 14 Jul 2020 11:58:39: Fewer paired peaks (871) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 871 pairs to build model! INFO @ Tue, 14 Jul 2020 11:58:39: start model_add_line... INFO @ Tue, 14 Jul 2020 11:58:39: start X-correlation... INFO @ Tue, 14 Jul 2020 11:58:39: end of X-cor INFO @ Tue, 14 Jul 2020 11:58:39: #2 finished! INFO @ Tue, 14 Jul 2020 11:58:39: #2 predicted fragment length is 69 bps INFO @ Tue, 14 Jul 2020 11:58:39: #2 alternative fragment length(s) may be 69 bps INFO @ Tue, 14 Jul 2020 11:58:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.10_model.r WARNING @ Tue, 14 Jul 2020 11:58:39: #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, 14 Jul 2020 11:58:39: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Tue, 14 Jul 2020 11:58:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:58:39: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:58:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:58:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.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, 14 Jul 2020 11:58:39: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:58:39: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:58:46: 1000000 INFO @ Tue, 14 Jul 2020 11:58:48: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:58:53: 2000000 INFO @ Tue, 14 Jul 2020 11:58:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:58:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:58:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.10_summits.bed INFO @ Tue, 14 Jul 2020 11:58:53: Done! pass1 - making usageList (148 chroms): 0 millis pass2 - checking and writing primary data (438 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:58:59: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:59:06: 4000000 INFO @ Tue, 14 Jul 2020 11:59:08: #1 tag size is determined as 68 bps INFO @ Tue, 14 Jul 2020 11:59:08: #1 tag size = 68 INFO @ Tue, 14 Jul 2020 11:59:08: #1 total tags in treatment: 4337149 INFO @ Tue, 14 Jul 2020 11:59:08: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:59:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 11:59:08: #1 tags after filtering in treatment: 4336920 INFO @ Tue, 14 Jul 2020 11:59:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:59:08: #1 finished! INFO @ Tue, 14 Jul 2020 11:59:08: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:59:08: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:59:09: #2 number of paired peaks: 871 WARNING @ Tue, 14 Jul 2020 11:59:09: Fewer paired peaks (871) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 871 pairs to build model! INFO @ Tue, 14 Jul 2020 11:59:09: start model_add_line... INFO @ Tue, 14 Jul 2020 11:59:09: start X-correlation... INFO @ Tue, 14 Jul 2020 11:59:09: end of X-cor INFO @ Tue, 14 Jul 2020 11:59:09: #2 finished! INFO @ Tue, 14 Jul 2020 11:59:09: #2 predicted fragment length is 69 bps INFO @ Tue, 14 Jul 2020 11:59:09: #2 alternative fragment length(s) may be 69 bps INFO @ Tue, 14 Jul 2020 11:59:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.20_model.r WARNING @ Tue, 14 Jul 2020 11:59:09: #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, 14 Jul 2020 11:59:09: #2 You may need to consider one of the other alternative d(s): 69 WARNING @ Tue, 14 Jul 2020 11:59:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 11:59:09: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:59:09: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:59:19: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:59:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:59:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:59:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521345/SRX8521345.20_summits.bed INFO @ Tue, 14 Jul 2020 11:59:23: Done! pass1 - making usageList (84 chroms): 0 millis pass2 - checking and writing primary data (154 records, 4 fields): 5 millis CompletedMACS2peakCalling