Job ID = 14168050 SRX = SRX8688942 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: 00:05:03 21750684 reads; of these: 21750684 (100.00%) were unpaired; of these: 7900769 (36.32%) aligned 0 times 10918319 (50.20%) aligned exactly 1 time 2931596 (13.48%) aligned >1 times 63.68% overall alignment rate Time searching: 00:05:03 Overall time: 00:05:03 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1176017 / 13849915 = 0.0849 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 14:51:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.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 @ Fri, 10 Dec 2021 14:51:37: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:51:37: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:51:42: 1000000 INFO @ Fri, 10 Dec 2021 14:51:47: 2000000 INFO @ Fri, 10 Dec 2021 14:51:52: 3000000 INFO @ Fri, 10 Dec 2021 14:51:57: 4000000 INFO @ Fri, 10 Dec 2021 14:52:02: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 14:52:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.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 @ Fri, 10 Dec 2021 14:52:07: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:52:07: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:52:07: 6000000 INFO @ Fri, 10 Dec 2021 14:52:12: 1000000 INFO @ Fri, 10 Dec 2021 14:52:12: 7000000 INFO @ Fri, 10 Dec 2021 14:52:18: 2000000 INFO @ Fri, 10 Dec 2021 14:52:18: 8000000 INFO @ Fri, 10 Dec 2021 14:52:23: 3000000 INFO @ Fri, 10 Dec 2021 14:52:23: 9000000 INFO @ Fri, 10 Dec 2021 14:52:28: 4000000 INFO @ Fri, 10 Dec 2021 14:52:29: 10000000 INFO @ Fri, 10 Dec 2021 14:52:34: 5000000 INFO @ Fri, 10 Dec 2021 14:52:34: 11000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 10 Dec 2021 14:52:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.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 @ Fri, 10 Dec 2021 14:52:37: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:52:37: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:52:39: 6000000 INFO @ Fri, 10 Dec 2021 14:52:40: 12000000 INFO @ Fri, 10 Dec 2021 14:52:43: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:52:43: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:52:43: #1 total tags in treatment: 12673898 INFO @ Fri, 10 Dec 2021 14:52:43: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:52:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 14:52:44: 1000000 INFO @ Fri, 10 Dec 2021 14:52:44: #1 tags after filtering in treatment: 12673832 INFO @ Fri, 10 Dec 2021 14:52:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:52:44: #1 finished! INFO @ Fri, 10 Dec 2021 14:52:44: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:52:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:52:45: 7000000 INFO @ Fri, 10 Dec 2021 14:52:45: #2 number of paired peaks: 309 WARNING @ Fri, 10 Dec 2021 14:52:45: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Fri, 10 Dec 2021 14:52:45: start model_add_line... INFO @ Fri, 10 Dec 2021 14:52:45: start X-correlation... INFO @ Fri, 10 Dec 2021 14:52:45: end of X-cor INFO @ Fri, 10 Dec 2021 14:52:45: #2 finished! INFO @ Fri, 10 Dec 2021 14:52:45: #2 predicted fragment length is 52 bps INFO @ Fri, 10 Dec 2021 14:52:45: #2 alternative fragment length(s) may be 4,52 bps INFO @ Fri, 10 Dec 2021 14:52:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.05_model.r WARNING @ Fri, 10 Dec 2021 14:52:45: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:52:45: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Fri, 10 Dec 2021 14:52:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 14:52:45: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:52:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:52:50: 2000000 INFO @ Fri, 10 Dec 2021 14:52:50: 8000000 INFO @ Fri, 10 Dec 2021 14:52:56: 9000000 INFO @ Fri, 10 Dec 2021 14:52:56: 3000000 INFO @ Fri, 10 Dec 2021 14:53:02: 10000000 INFO @ Fri, 10 Dec 2021 14:53:03: 4000000 INFO @ Fri, 10 Dec 2021 14:53:07: 11000000 INFO @ Fri, 10 Dec 2021 14:53:08: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:53:09: 5000000 INFO @ Fri, 10 Dec 2021 14:53:13: 12000000 INFO @ Fri, 10 Dec 2021 14:53:16: 6000000 INFO @ Fri, 10 Dec 2021 14:53:17: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:53:17: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:53:17: #1 total tags in treatment: 12673898 INFO @ Fri, 10 Dec 2021 14:53:17: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:53:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 14:53:17: #1 tags after filtering in treatment: 12673832 INFO @ Fri, 10 Dec 2021 14:53:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:53:17: #1 finished! INFO @ Fri, 10 Dec 2021 14:53:17: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:53:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:53:18: #2 number of paired peaks: 309 WARNING @ Fri, 10 Dec 2021 14:53:18: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Fri, 10 Dec 2021 14:53:18: start model_add_line... INFO @ Fri, 10 Dec 2021 14:53:18: start X-correlation... INFO @ Fri, 10 Dec 2021 14:53:18: end of X-cor INFO @ Fri, 10 Dec 2021 14:53:18: #2 finished! INFO @ Fri, 10 Dec 2021 14:53:18: #2 predicted fragment length is 52 bps INFO @ Fri, 10 Dec 2021 14:53:18: #2 alternative fragment length(s) may be 4,52 bps INFO @ Fri, 10 Dec 2021 14:53:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.10_model.r WARNING @ Fri, 10 Dec 2021 14:53:18: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:53:18: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Fri, 10 Dec 2021 14:53:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 14:53:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:53:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:53:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.05_peaks.xls INFO @ Fri, 10 Dec 2021 14:53:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:53:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.05_summits.bed INFO @ Fri, 10 Dec 2021 14:53:20: Done! pass1 - making usageList (491 chroms): 1 millis pass2 - checking and writing primary data (1747 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:53:22: 7000000 INFO @ Fri, 10 Dec 2021 14:53:28: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 14:53:34: 9000000 INFO @ Fri, 10 Dec 2021 14:53:41: 10000000 INFO @ Fri, 10 Dec 2021 14:53:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:53:47: 11000000 INFO @ Fri, 10 Dec 2021 14:53:53: 12000000 INFO @ Fri, 10 Dec 2021 14:53:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.10_peaks.xls INFO @ Fri, 10 Dec 2021 14:53:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:53:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.10_summits.bed INFO @ Fri, 10 Dec 2021 14:53:55: Done! pass1 - making usageList (312 chroms): 1 millis pass2 - checking and writing primary data (803 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:53:57: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:53:57: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:53:57: #1 total tags in treatment: 12673898 INFO @ Fri, 10 Dec 2021 14:53:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:53:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 14:53:57: #1 tags after filtering in treatment: 12673832 INFO @ Fri, 10 Dec 2021 14:53:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:53:57: #1 finished! INFO @ Fri, 10 Dec 2021 14:53:57: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:53:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:53:58: #2 number of paired peaks: 309 WARNING @ Fri, 10 Dec 2021 14:53:58: Fewer paired peaks (309) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 309 pairs to build model! INFO @ Fri, 10 Dec 2021 14:53:58: start model_add_line... INFO @ Fri, 10 Dec 2021 14:53:58: start X-correlation... INFO @ Fri, 10 Dec 2021 14:53:58: end of X-cor INFO @ Fri, 10 Dec 2021 14:53:58: #2 finished! INFO @ Fri, 10 Dec 2021 14:53:58: #2 predicted fragment length is 52 bps INFO @ Fri, 10 Dec 2021 14:53:58: #2 alternative fragment length(s) may be 4,52 bps INFO @ Fri, 10 Dec 2021 14:53:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.20_model.r WARNING @ Fri, 10 Dec 2021 14:53:58: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:53:58: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Fri, 10 Dec 2021 14:53:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 14:53:58: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:53:58: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 14:54:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:54:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.20_peaks.xls INFO @ Fri, 10 Dec 2021 14:54:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:54:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688942/SRX8688942.20_summits.bed INFO @ Fri, 10 Dec 2021 14:54:34: Done! pass1 - making usageList (126 chroms): 1 millis pass2 - checking and writing primary data (229 records, 4 fields): 5 millis CompletedMACS2peakCalling