Job ID = 16439472 SRX = SRX11965413 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:19 12722727 reads; of these: 12722727 (100.00%) were unpaired; of these: 4547564 (35.74%) aligned 0 times 6285821 (49.41%) aligned exactly 1 time 1889342 (14.85%) aligned >1 times 64.26% overall alignment rate Time searching: 00:04:20 Overall time: 00:04:20 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] 5639724 / 8175163 = 0.6899 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:24:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.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, 02 Aug 2022 15:24:37: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:24:37: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:24:47: 1000000 INFO @ Tue, 02 Aug 2022 15:24:58: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:25:03: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 15:25:03: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 15:25:03: #1 total tags in treatment: 2535439 INFO @ Tue, 02 Aug 2022 15:25:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:25:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:25:03: #1 tags after filtering in treatment: 2535192 INFO @ Tue, 02 Aug 2022 15:25:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:25:03: #1 finished! INFO @ Tue, 02 Aug 2022 15:25:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:25:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:25:03: #2 number of paired peaks: 605 WARNING @ Tue, 02 Aug 2022 15:25:03: Fewer paired peaks (605) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 605 pairs to build model! INFO @ Tue, 02 Aug 2022 15:25:03: start model_add_line... INFO @ Tue, 02 Aug 2022 15:25:03: start X-correlation... INFO @ Tue, 02 Aug 2022 15:25:04: end of X-cor INFO @ Tue, 02 Aug 2022 15:25:04: #2 finished! INFO @ Tue, 02 Aug 2022 15:25:04: #2 predicted fragment length is 57 bps INFO @ Tue, 02 Aug 2022 15:25:04: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 02 Aug 2022 15:25:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.05_model.r WARNING @ Tue, 02 Aug 2022 15:25:04: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:25:04: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 02 Aug 2022 15:25:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:25:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:25:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:25:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.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, 02 Aug 2022 15:25:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:25:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:25:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:25:15: 1000000 INFO @ Tue, 02 Aug 2022 15:25:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.05_peaks.xls INFO @ Tue, 02 Aug 2022 15:25:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:25:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.05_summits.bed INFO @ Tue, 02 Aug 2022 15:25:17: Done! pass1 - making usageList (246 chroms): 3 millis pass2 - checking and writing primary data (618 records, 4 fields): 32 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 15:25:25: 2000000 INFO @ Tue, 02 Aug 2022 15:25:31: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 15:25:31: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 15:25:31: #1 total tags in treatment: 2535439 INFO @ Tue, 02 Aug 2022 15:25:31: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:25:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:25:31: #1 tags after filtering in treatment: 2535192 INFO @ Tue, 02 Aug 2022 15:25:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:25:31: #1 finished! INFO @ Tue, 02 Aug 2022 15:25:31: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:25:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:25:31: #2 number of paired peaks: 605 WARNING @ Tue, 02 Aug 2022 15:25:31: Fewer paired peaks (605) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 605 pairs to build model! INFO @ Tue, 02 Aug 2022 15:25:31: start model_add_line... INFO @ Tue, 02 Aug 2022 15:25:31: start X-correlation... INFO @ Tue, 02 Aug 2022 15:25:31: end of X-cor INFO @ Tue, 02 Aug 2022 15:25:31: #2 finished! INFO @ Tue, 02 Aug 2022 15:25:31: #2 predicted fragment length is 57 bps INFO @ Tue, 02 Aug 2022 15:25:31: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 02 Aug 2022 15:25:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.10_model.r WARNING @ Tue, 02 Aug 2022 15:25:32: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:25:32: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 02 Aug 2022 15:25:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:25:32: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:25:32: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 15:25:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.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, 02 Aug 2022 15:25:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 15:25:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 15:25:41: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:25:45: 1000000 INFO @ Tue, 02 Aug 2022 15:25:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.10_peaks.xls INFO @ Tue, 02 Aug 2022 15:25:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:25:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.10_summits.bed INFO @ Tue, 02 Aug 2022 15:25:45: Done! pass1 - making usageList (136 chroms): 4 millis pass2 - checking and writing primary data (384 records, 4 fields): 28 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 15:25:55: 2000000 BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 15:26:00: #1 tag size is determined as 51 bps INFO @ Tue, 02 Aug 2022 15:26:00: #1 tag size = 51 INFO @ Tue, 02 Aug 2022 15:26:00: #1 total tags in treatment: 2535439 INFO @ Tue, 02 Aug 2022 15:26:00: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 15:26:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 15:26:01: #1 tags after filtering in treatment: 2535192 INFO @ Tue, 02 Aug 2022 15:26:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 15:26:01: #1 finished! INFO @ Tue, 02 Aug 2022 15:26:01: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 15:26:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 15:26:01: #2 number of paired peaks: 605 WARNING @ Tue, 02 Aug 2022 15:26:01: Fewer paired peaks (605) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 605 pairs to build model! INFO @ Tue, 02 Aug 2022 15:26:01: start model_add_line... INFO @ Tue, 02 Aug 2022 15:26:01: start X-correlation... INFO @ Tue, 02 Aug 2022 15:26:01: end of X-cor INFO @ Tue, 02 Aug 2022 15:26:01: #2 finished! INFO @ Tue, 02 Aug 2022 15:26:01: #2 predicted fragment length is 57 bps INFO @ Tue, 02 Aug 2022 15:26:01: #2 alternative fragment length(s) may be 57 bps INFO @ Tue, 02 Aug 2022 15:26:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.20_model.r WARNING @ Tue, 02 Aug 2022 15:26:01: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 15:26:01: #2 You may need to consider one of the other alternative d(s): 57 WARNING @ Tue, 02 Aug 2022 15:26:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 15:26:01: #3 Call peaks... INFO @ Tue, 02 Aug 2022 15:26:01: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 15:26:10: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 15:26:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.20_peaks.xls INFO @ Tue, 02 Aug 2022 15:26:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 15:26:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX11965413/SRX11965413.20_summits.bed INFO @ Tue, 02 Aug 2022 15:26:14: Done! pass1 - making usageList (125 chroms): 1 millis pass2 - checking and writing primary data (304 records, 4 fields): 20 millis CompletedMACS2peakCalling