Job ID = 6529320 SRX = SRX1743169 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: 00:01:00 4090239 reads; of these: 4090239 (100.00%) were unpaired; of these: 1958486 (47.88%) aligned 0 times 1909450 (46.68%) aligned exactly 1 time 222303 (5.43%) aligned >1 times 52.12% overall alignment rate Time searching: 00:01:00 Overall time: 00:01:00 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] 351716 / 2131753 = 0.1650 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 01:46:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.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 01:46:43: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:46:43: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:46:50: 1000000 INFO @ Tue, 30 Jun 2020 01:46:56: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 01:46:56: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 01:46:56: #1 total tags in treatment: 1780037 INFO @ Tue, 30 Jun 2020 01:46:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:46:56: #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 01:46:56: #1 tags after filtering in treatment: 1779543 INFO @ Tue, 30 Jun 2020 01:46:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:46:56: #1 finished! INFO @ Tue, 30 Jun 2020 01:46:56: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:46:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:46:56: #2 number of paired peaks: 185 WARNING @ Tue, 30 Jun 2020 01:46:56: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Tue, 30 Jun 2020 01:46:56: start model_add_line... INFO @ Tue, 30 Jun 2020 01:46:56: start X-correlation... INFO @ Tue, 30 Jun 2020 01:46:56: end of X-cor INFO @ Tue, 30 Jun 2020 01:46:56: #2 finished! INFO @ Tue, 30 Jun 2020 01:46:56: #2 predicted fragment length is 79 bps INFO @ Tue, 30 Jun 2020 01:46:56: #2 alternative fragment length(s) may be 79,98,417,435,450,478,507,526,545,560,590,598 bps INFO @ Tue, 30 Jun 2020 01:46:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.05_model.r WARNING @ Tue, 30 Jun 2020 01:46:56: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:46:56: #2 You may need to consider one of the other alternative d(s): 79,98,417,435,450,478,507,526,545,560,590,598 WARNING @ Tue, 30 Jun 2020 01:46:56: #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 01:46:56: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:46:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:47:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:47:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.05_peaks.xls INFO @ Tue, 30 Jun 2020 01:47:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:47:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.05_summits.bed INFO @ Tue, 30 Jun 2020 01:47:03: Done! pass1 - making usageList (64 chroms): 1 millis pass2 - checking and writing primary data (114 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 01:47:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.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 01:47:13: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:47:13: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:47:20: 1000000 INFO @ Tue, 30 Jun 2020 01:47:26: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 01:47:26: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 01:47:26: #1 total tags in treatment: 1780037 INFO @ Tue, 30 Jun 2020 01:47:26: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:47:26: #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 01:47:27: #1 tags after filtering in treatment: 1779543 INFO @ Tue, 30 Jun 2020 01:47:27: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:47:27: #1 finished! INFO @ Tue, 30 Jun 2020 01:47:27: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:47:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:47:27: #2 number of paired peaks: 185 WARNING @ Tue, 30 Jun 2020 01:47:27: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Tue, 30 Jun 2020 01:47:27: start model_add_line... INFO @ Tue, 30 Jun 2020 01:47:27: start X-correlation... INFO @ Tue, 30 Jun 2020 01:47:27: end of X-cor INFO @ Tue, 30 Jun 2020 01:47:27: #2 finished! INFO @ Tue, 30 Jun 2020 01:47:27: #2 predicted fragment length is 79 bps INFO @ Tue, 30 Jun 2020 01:47:27: #2 alternative fragment length(s) may be 79,98,417,435,450,478,507,526,545,560,590,598 bps INFO @ Tue, 30 Jun 2020 01:47:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.10_model.r WARNING @ Tue, 30 Jun 2020 01:47:27: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:47:27: #2 You may need to consider one of the other alternative d(s): 79,98,417,435,450,478,507,526,545,560,590,598 WARNING @ Tue, 30 Jun 2020 01:47:27: #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 01:47:27: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:47:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 01:47:32: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:47:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.10_peaks.xls INFO @ Tue, 30 Jun 2020 01:47:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:47:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.10_summits.bed INFO @ Tue, 30 Jun 2020 01:47:34: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (68 records, 4 fields): 4 millis CompletedMACS2peakCalling 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 01:47:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.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 01:47:44: #1 read tag files... INFO @ Tue, 30 Jun 2020 01:47:44: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 01:47:50: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 01:47:55: #1 tag size is determined as 75 bps INFO @ Tue, 30 Jun 2020 01:47:55: #1 tag size = 75 INFO @ Tue, 30 Jun 2020 01:47:55: #1 total tags in treatment: 1780037 INFO @ Tue, 30 Jun 2020 01:47:55: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 01:47:55: #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 01:47:55: #1 tags after filtering in treatment: 1779543 INFO @ Tue, 30 Jun 2020 01:47:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 01:47:55: #1 finished! INFO @ Tue, 30 Jun 2020 01:47:55: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 01:47:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 01:47:56: #2 number of paired peaks: 185 WARNING @ Tue, 30 Jun 2020 01:47:56: Fewer paired peaks (185) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 185 pairs to build model! INFO @ Tue, 30 Jun 2020 01:47:56: start model_add_line... INFO @ Tue, 30 Jun 2020 01:47:56: start X-correlation... INFO @ Tue, 30 Jun 2020 01:47:56: end of X-cor INFO @ Tue, 30 Jun 2020 01:47:56: #2 finished! INFO @ Tue, 30 Jun 2020 01:47:56: #2 predicted fragment length is 79 bps INFO @ Tue, 30 Jun 2020 01:47:56: #2 alternative fragment length(s) may be 79,98,417,435,450,478,507,526,545,560,590,598 bps INFO @ Tue, 30 Jun 2020 01:47:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.20_model.r WARNING @ Tue, 30 Jun 2020 01:47:56: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 30 Jun 2020 01:47:56: #2 You may need to consider one of the other alternative d(s): 79,98,417,435,450,478,507,526,545,560,590,598 WARNING @ Tue, 30 Jun 2020 01:47:56: #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 01:47:56: #3 Call peaks... INFO @ Tue, 30 Jun 2020 01:47:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 01:48:00: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 01:48:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.20_peaks.xls INFO @ Tue, 30 Jun 2020 01:48:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 01:48:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1743169/SRX1743169.20_summits.bed INFO @ Tue, 30 Jun 2020 01:48:02: Done! pass1 - making usageList (21 chroms): 1 millis pass2 - checking and writing primary data (26 records, 4 fields): 2 millis CompletedMACS2peakCalling