Job ID = 12265082 SRX = SRX2661684 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: 00:05:56 20302186 reads; of these: 20302186 (100.00%) were unpaired; of these: 1451281 (7.15%) aligned 0 times 16009575 (78.86%) aligned exactly 1 time 2841330 (14.00%) aligned >1 times 92.85% overall alignment rate Time searching: 00:05:56 Overall time: 00:05:56 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] 8676816 / 18850905 = 0.4603 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:17:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.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 @ Sat, 03 Apr 2021 06:17:23: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:17:23: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:17:34: 1000000 INFO @ Sat, 03 Apr 2021 06:17:45: 2000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:17:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.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 @ Sat, 03 Apr 2021 06:17:53: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:17:53: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:17:56: 3000000 INFO @ Sat, 03 Apr 2021 06:18:05: 1000000 INFO @ Sat, 03 Apr 2021 06:18:07: 4000000 INFO @ Sat, 03 Apr 2021 06:18:17: 2000000 INFO @ Sat, 03 Apr 2021 06:18:17: 5000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:18:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.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 @ Sat, 03 Apr 2021 06:18:23: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:18:23: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:18:28: 3000000 INFO @ Sat, 03 Apr 2021 06:18:28: 6000000 INFO @ Sat, 03 Apr 2021 06:18:33: 1000000 INFO @ Sat, 03 Apr 2021 06:18:38: 4000000 INFO @ Sat, 03 Apr 2021 06:18:39: 7000000 INFO @ Sat, 03 Apr 2021 06:18:42: 2000000 INFO @ Sat, 03 Apr 2021 06:18:49: 5000000 INFO @ Sat, 03 Apr 2021 06:18:50: 8000000 INFO @ Sat, 03 Apr 2021 06:18:52: 3000000 INFO @ Sat, 03 Apr 2021 06:19:01: 6000000 INFO @ Sat, 03 Apr 2021 06:19:02: 4000000 INFO @ Sat, 03 Apr 2021 06:19:03: 9000000 INFO @ Sat, 03 Apr 2021 06:19:11: 5000000 INFO @ Sat, 03 Apr 2021 06:19:12: 7000000 INFO @ Sat, 03 Apr 2021 06:19:15: 10000000 INFO @ Sat, 03 Apr 2021 06:19:17: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:19:17: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:19:17: #1 total tags in treatment: 10174089 INFO @ Sat, 03 Apr 2021 06:19:17: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:19:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:19:17: #1 tags after filtering in treatment: 10174081 INFO @ Sat, 03 Apr 2021 06:19:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:19:17: #1 finished! INFO @ Sat, 03 Apr 2021 06:19:17: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:19:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:19:18: #2 number of paired peaks: 557 WARNING @ Sat, 03 Apr 2021 06:19:18: Fewer paired peaks (557) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 557 pairs to build model! INFO @ Sat, 03 Apr 2021 06:19:18: start model_add_line... INFO @ Sat, 03 Apr 2021 06:19:18: start X-correlation... INFO @ Sat, 03 Apr 2021 06:19:18: end of X-cor INFO @ Sat, 03 Apr 2021 06:19:18: #2 finished! INFO @ Sat, 03 Apr 2021 06:19:18: #2 predicted fragment length is 78 bps INFO @ Sat, 03 Apr 2021 06:19:18: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 03 Apr 2021 06:19:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.05_model.r WARNING @ Sat, 03 Apr 2021 06:19:18: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:19:18: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 03 Apr 2021 06:19:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:19:18: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:19:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:19:20: 6000000 INFO @ Sat, 03 Apr 2021 06:19:22: 8000000 INFO @ Sat, 03 Apr 2021 06:19:29: 7000000 INFO @ Sat, 03 Apr 2021 06:19:35: 9000000 INFO @ Sat, 03 Apr 2021 06:19:38: 8000000 INFO @ Sat, 03 Apr 2021 06:19:46: 10000000 INFO @ Sat, 03 Apr 2021 06:19:48: 9000000 INFO @ Sat, 03 Apr 2021 06:19:48: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:19:48: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:19:48: #1 total tags in treatment: 10174089 INFO @ Sat, 03 Apr 2021 06:19:48: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:19:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:19:49: #1 tags after filtering in treatment: 10174081 INFO @ Sat, 03 Apr 2021 06:19:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:19:49: #1 finished! INFO @ Sat, 03 Apr 2021 06:19:49: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:19:49: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:19:50: #2 number of paired peaks: 557 WARNING @ Sat, 03 Apr 2021 06:19:50: Fewer paired peaks (557) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 557 pairs to build model! INFO @ Sat, 03 Apr 2021 06:19:50: start model_add_line... INFO @ Sat, 03 Apr 2021 06:19:50: start X-correlation... INFO @ Sat, 03 Apr 2021 06:19:50: end of X-cor INFO @ Sat, 03 Apr 2021 06:19:50: #2 finished! INFO @ Sat, 03 Apr 2021 06:19:50: #2 predicted fragment length is 78 bps INFO @ Sat, 03 Apr 2021 06:19:50: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 03 Apr 2021 06:19:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.10_model.r WARNING @ Sat, 03 Apr 2021 06:19:50: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:19:50: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 03 Apr 2021 06:19:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:19:50: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:19:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:19:51: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:19:59: 10000000 INFO @ Sat, 03 Apr 2021 06:20:01: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:20:01: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:20:01: #1 total tags in treatment: 10174089 INFO @ Sat, 03 Apr 2021 06:20:01: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:20:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:20:01: #1 tags after filtering in treatment: 10174081 INFO @ Sat, 03 Apr 2021 06:20:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:20:01: #1 finished! INFO @ Sat, 03 Apr 2021 06:20:01: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:20:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:20:02: #2 number of paired peaks: 557 WARNING @ Sat, 03 Apr 2021 06:20:02: Fewer paired peaks (557) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 557 pairs to build model! INFO @ Sat, 03 Apr 2021 06:20:02: start model_add_line... INFO @ Sat, 03 Apr 2021 06:20:02: start X-correlation... INFO @ Sat, 03 Apr 2021 06:20:02: end of X-cor INFO @ Sat, 03 Apr 2021 06:20:02: #2 finished! INFO @ Sat, 03 Apr 2021 06:20:02: #2 predicted fragment length is 78 bps INFO @ Sat, 03 Apr 2021 06:20:02: #2 alternative fragment length(s) may be 78 bps INFO @ Sat, 03 Apr 2021 06:20:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.20_model.r WARNING @ Sat, 03 Apr 2021 06:20:02: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:20:02: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Sat, 03 Apr 2021 06:20:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:20:02: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:20:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:20:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:20:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:20:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.05_summits.bed INFO @ Sat, 03 Apr 2021 06:20:08: Done! pass1 - making usageList (276 chroms): 4 millis pass2 - checking and writing primary data (11763 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:20:22: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:20:34: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:20:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:20:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:20:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.10_summits.bed INFO @ Sat, 03 Apr 2021 06:20:38: Done! pass1 - making usageList (175 chroms): 3 millis pass2 - checking and writing primary data (5796 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:20:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:20:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:20:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2661684/SRX2661684.20_summits.bed INFO @ Sat, 03 Apr 2021 06:20:51: Done! pass1 - making usageList (101 chroms): 3 millis pass2 - checking and writing primary data (1420 records, 4 fields): 14 millis CompletedMACS2peakCalling