Job ID = 6627425 SRX = SRX8521294 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: 00:07:45 52854416 reads; of these: 52854416 (100.00%) were unpaired; of these: 45089957 (85.31%) aligned 0 times 5914199 (11.19%) aligned exactly 1 time 1850260 (3.50%) aligned >1 times 14.69% overall alignment rate Time searching: 00:07:45 Overall time: 00:07:45 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] 1283540 / 7764459 = 0.1653 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 11:33:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.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 11:33:09: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:33:09: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:33:15: 1000000 INFO @ Tue, 14 Jul 2020 11:33:21: 2000000 INFO @ Tue, 14 Jul 2020 11:33:27: 3000000 INFO @ Tue, 14 Jul 2020 11:33:32: 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 11:33:38: 5000000 INFO @ Tue, 14 Jul 2020 11:33:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.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 11:33:39: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:33:39: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:33:45: 6000000 INFO @ Tue, 14 Jul 2020 11:33:46: 1000000 INFO @ Tue, 14 Jul 2020 11:33:48: #1 tag size is determined as 61 bps INFO @ Tue, 14 Jul 2020 11:33:48: #1 tag size = 61 INFO @ Tue, 14 Jul 2020 11:33:48: #1 total tags in treatment: 6480919 INFO @ Tue, 14 Jul 2020 11:33:48: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:33:48: #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 11:33:49: #1 tags after filtering in treatment: 6480712 INFO @ Tue, 14 Jul 2020 11:33:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:33:49: #1 finished! INFO @ Tue, 14 Jul 2020 11:33:49: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:33:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:33:49: #2 number of paired peaks: 588 WARNING @ Tue, 14 Jul 2020 11:33:49: Fewer paired peaks (588) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 588 pairs to build model! INFO @ Tue, 14 Jul 2020 11:33:49: start model_add_line... INFO @ Tue, 14 Jul 2020 11:33:49: start X-correlation... INFO @ Tue, 14 Jul 2020 11:33:49: end of X-cor INFO @ Tue, 14 Jul 2020 11:33:49: #2 finished! INFO @ Tue, 14 Jul 2020 11:33:49: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 11:33:49: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 11:33:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.05_model.r WARNING @ Tue, 14 Jul 2020 11:33:49: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:33:49: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 11:33:49: #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 11:33:49: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:33:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:33:53: 2000000 INFO @ Tue, 14 Jul 2020 11:33:59: 3000000 INFO @ Tue, 14 Jul 2020 11:34:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:34:05: 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 11:34:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.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 11:34:09: #1 read tag files... INFO @ Tue, 14 Jul 2020 11:34:09: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 11:34:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.05_peaks.xls INFO @ Tue, 14 Jul 2020 11:34:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:34:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.05_summits.bed INFO @ Tue, 14 Jul 2020 11:34:10: Done! pass1 - making usageList (218 chroms): 1 millis pass2 - checking and writing primary data (1573 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 11:34:12: 5000000 INFO @ Tue, 14 Jul 2020 11:34:17: 1000000 INFO @ Tue, 14 Jul 2020 11:34:19: 6000000 INFO @ Tue, 14 Jul 2020 11:34:22: #1 tag size is determined as 61 bps INFO @ Tue, 14 Jul 2020 11:34:22: #1 tag size = 61 INFO @ Tue, 14 Jul 2020 11:34:22: #1 total tags in treatment: 6480919 INFO @ Tue, 14 Jul 2020 11:34:22: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:34:22: #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 11:34:22: #1 tags after filtering in treatment: 6480712 INFO @ Tue, 14 Jul 2020 11:34:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:34:22: #1 finished! INFO @ Tue, 14 Jul 2020 11:34:22: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:34:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:34:23: #2 number of paired peaks: 588 WARNING @ Tue, 14 Jul 2020 11:34:23: Fewer paired peaks (588) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 588 pairs to build model! INFO @ Tue, 14 Jul 2020 11:34:23: start model_add_line... INFO @ Tue, 14 Jul 2020 11:34:23: start X-correlation... INFO @ Tue, 14 Jul 2020 11:34:23: end of X-cor INFO @ Tue, 14 Jul 2020 11:34:23: #2 finished! INFO @ Tue, 14 Jul 2020 11:34:23: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 11:34:23: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 11:34:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.10_model.r WARNING @ Tue, 14 Jul 2020 11:34:23: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:34:23: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 11:34:23: #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 11:34:23: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:34:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 11:34:24: 2000000 INFO @ Tue, 14 Jul 2020 11:34:32: 3000000 INFO @ Tue, 14 Jul 2020 11:34:36: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:34:38: 4000000 INFO @ Tue, 14 Jul 2020 11:34:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.10_peaks.xls INFO @ Tue, 14 Jul 2020 11:34:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:34:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.10_summits.bed INFO @ Tue, 14 Jul 2020 11:34:43: Done! pass1 - making usageList (129 chroms): 1 millis pass2 - checking and writing primary data (487 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 11:34:45: 5000000 INFO @ Tue, 14 Jul 2020 11:34:53: 6000000 INFO @ Tue, 14 Jul 2020 11:34:56: #1 tag size is determined as 61 bps INFO @ Tue, 14 Jul 2020 11:34:56: #1 tag size = 61 INFO @ Tue, 14 Jul 2020 11:34:56: #1 total tags in treatment: 6480919 INFO @ Tue, 14 Jul 2020 11:34:56: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 11:34:56: #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 11:34:56: #1 tags after filtering in treatment: 6480712 INFO @ Tue, 14 Jul 2020 11:34:56: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 11:34:56: #1 finished! INFO @ Tue, 14 Jul 2020 11:34:56: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 11:34:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 11:34:57: #2 number of paired peaks: 588 WARNING @ Tue, 14 Jul 2020 11:34:57: Fewer paired peaks (588) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 588 pairs to build model! INFO @ Tue, 14 Jul 2020 11:34:57: start model_add_line... INFO @ Tue, 14 Jul 2020 11:34:57: start X-correlation... INFO @ Tue, 14 Jul 2020 11:34:57: end of X-cor INFO @ Tue, 14 Jul 2020 11:34:57: #2 finished! INFO @ Tue, 14 Jul 2020 11:34:57: #2 predicted fragment length is 59 bps INFO @ Tue, 14 Jul 2020 11:34:57: #2 alternative fragment length(s) may be 59 bps INFO @ Tue, 14 Jul 2020 11:34:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.20_model.r WARNING @ Tue, 14 Jul 2020 11:34:57: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 11:34:57: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Tue, 14 Jul 2020 11:34:57: #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 11:34:57: #3 Call peaks... INFO @ Tue, 14 Jul 2020 11:34:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 11:35:11: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 11:35:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.20_peaks.xls INFO @ Tue, 14 Jul 2020 11:35:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 11:35:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8521294/SRX8521294.20_summits.bed INFO @ Tue, 14 Jul 2020 11:35:18: Done! pass1 - making usageList (79 chroms): 1 millis pass2 - checking and writing primary data (147 records, 4 fields): 4 millis CompletedMACS2peakCalling