Job ID = 12265444 SRX = SRX5010755 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: 00:08:24 33979005 reads; of these: 33979005 (100.00%) were unpaired; of these: 1170681 (3.45%) aligned 0 times 26911525 (79.20%) aligned exactly 1 time 5896799 (17.35%) aligned >1 times 96.55% overall alignment rate Time searching: 00:08:24 Overall time: 00:08:24 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 16 files... [bam_rmdupse_core] 20167950 / 32808324 = 0.6147 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 07:17:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.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 07:17:15: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:17:15: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:17:20: 1000000 INFO @ Sat, 03 Apr 2021 07:17:26: 2000000 INFO @ Sat, 03 Apr 2021 07:17:31: 3000000 INFO @ Sat, 03 Apr 2021 07:17:36: 4000000 INFO @ Sat, 03 Apr 2021 07:17:41: 5000000 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 07:17:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.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 07:17:45: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:17:45: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:17:47: 6000000 INFO @ Sat, 03 Apr 2021 07:17:50: 1000000 INFO @ Sat, 03 Apr 2021 07:17:52: 7000000 INFO @ Sat, 03 Apr 2021 07:17:56: 2000000 INFO @ Sat, 03 Apr 2021 07:17:58: 8000000 INFO @ Sat, 03 Apr 2021 07:18:01: 3000000 INFO @ Sat, 03 Apr 2021 07:18:03: 9000000 INFO @ Sat, 03 Apr 2021 07:18:07: 4000000 INFO @ Sat, 03 Apr 2021 07:18:09: 10000000 INFO @ Sat, 03 Apr 2021 07:18:12: 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 07:18:14: 11000000 INFO @ Sat, 03 Apr 2021 07:18:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.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 07:18:15: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:18:15: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:18:17: 6000000 INFO @ Sat, 03 Apr 2021 07:18:20: 12000000 INFO @ Sat, 03 Apr 2021 07:18:20: 1000000 INFO @ Sat, 03 Apr 2021 07:18:23: 7000000 INFO @ Sat, 03 Apr 2021 07:18:23: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:18:23: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:18:23: #1 total tags in treatment: 12640374 INFO @ Sat, 03 Apr 2021 07:18:23: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:18:23: #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 07:18:24: #1 tags after filtering in treatment: 12640290 INFO @ Sat, 03 Apr 2021 07:18:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:18:24: #1 finished! INFO @ Sat, 03 Apr 2021 07:18:24: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:18:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:18:25: #2 number of paired peaks: 768 WARNING @ Sat, 03 Apr 2021 07:18:25: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Sat, 03 Apr 2021 07:18:25: start model_add_line... INFO @ Sat, 03 Apr 2021 07:18:25: start X-correlation... INFO @ Sat, 03 Apr 2021 07:18:25: end of X-cor INFO @ Sat, 03 Apr 2021 07:18:25: #2 finished! INFO @ Sat, 03 Apr 2021 07:18:25: #2 predicted fragment length is 68 bps INFO @ Sat, 03 Apr 2021 07:18:25: #2 alternative fragment length(s) may be 68 bps INFO @ Sat, 03 Apr 2021 07:18:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.05_model.r WARNING @ Sat, 03 Apr 2021 07:18:25: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:18:25: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sat, 03 Apr 2021 07:18:25: #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 07:18:25: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:18:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:18:26: 2000000 INFO @ Sat, 03 Apr 2021 07:18:28: 8000000 INFO @ Sat, 03 Apr 2021 07:18:31: 3000000 INFO @ Sat, 03 Apr 2021 07:18:34: 9000000 INFO @ Sat, 03 Apr 2021 07:18:37: 4000000 INFO @ Sat, 03 Apr 2021 07:18:40: 10000000 INFO @ Sat, 03 Apr 2021 07:18:42: 5000000 INFO @ Sat, 03 Apr 2021 07:18:45: 11000000 INFO @ Sat, 03 Apr 2021 07:18:48: 6000000 INFO @ Sat, 03 Apr 2021 07:18:50: 12000000 INFO @ Sat, 03 Apr 2021 07:18:52: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:18:53: 7000000 INFO @ Sat, 03 Apr 2021 07:18:54: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:18:54: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:18:54: #1 total tags in treatment: 12640374 INFO @ Sat, 03 Apr 2021 07:18:54: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:18:54: #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 07:18:55: #1 tags after filtering in treatment: 12640290 INFO @ Sat, 03 Apr 2021 07:18:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:18:55: #1 finished! INFO @ Sat, 03 Apr 2021 07:18:55: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:18:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:18:56: #2 number of paired peaks: 768 WARNING @ Sat, 03 Apr 2021 07:18:56: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Sat, 03 Apr 2021 07:18:56: start model_add_line... INFO @ Sat, 03 Apr 2021 07:18:56: start X-correlation... INFO @ Sat, 03 Apr 2021 07:18:56: end of X-cor INFO @ Sat, 03 Apr 2021 07:18:56: #2 finished! INFO @ Sat, 03 Apr 2021 07:18:56: #2 predicted fragment length is 68 bps INFO @ Sat, 03 Apr 2021 07:18:56: #2 alternative fragment length(s) may be 68 bps INFO @ Sat, 03 Apr 2021 07:18:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.10_model.r WARNING @ Sat, 03 Apr 2021 07:18:56: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:18:56: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sat, 03 Apr 2021 07:18:56: #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 07:18:56: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:18:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:18:59: 8000000 INFO @ Sat, 03 Apr 2021 07:19:04: 9000000 INFO @ Sat, 03 Apr 2021 07:19:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:19:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:19:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.05_summits.bed INFO @ Sat, 03 Apr 2021 07:19:07: Done! pass1 - making usageList (492 chroms): 3 millis pass2 - checking and writing primary data (8180 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:19:10: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:19:15: 11000000 INFO @ Sat, 03 Apr 2021 07:19:20: 12000000 INFO @ Sat, 03 Apr 2021 07:19:23: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:19:23: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 07:19:23: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 07:19:23: #1 total tags in treatment: 12640374 INFO @ Sat, 03 Apr 2021 07:19:23: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:19:23: #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 07:19:24: #1 tags after filtering in treatment: 12640290 INFO @ Sat, 03 Apr 2021 07:19:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 07:19:24: #1 finished! INFO @ Sat, 03 Apr 2021 07:19:24: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:19:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:19:25: #2 number of paired peaks: 768 WARNING @ Sat, 03 Apr 2021 07:19:25: Fewer paired peaks (768) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 768 pairs to build model! INFO @ Sat, 03 Apr 2021 07:19:25: start model_add_line... INFO @ Sat, 03 Apr 2021 07:19:25: start X-correlation... INFO @ Sat, 03 Apr 2021 07:19:25: end of X-cor INFO @ Sat, 03 Apr 2021 07:19:25: #2 finished! INFO @ Sat, 03 Apr 2021 07:19:25: #2 predicted fragment length is 68 bps INFO @ Sat, 03 Apr 2021 07:19:25: #2 alternative fragment length(s) may be 68 bps INFO @ Sat, 03 Apr 2021 07:19:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.20_model.r WARNING @ Sat, 03 Apr 2021 07:19:25: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:19:25: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sat, 03 Apr 2021 07:19:25: #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 07:19:25: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:19:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:19:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:19:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:19:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.10_summits.bed INFO @ Sat, 03 Apr 2021 07:19:37: Done! pass1 - making usageList (316 chroms): 1 millis pass2 - checking and writing primary data (3951 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:19:53: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:20:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:20:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:20:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5010755/SRX5010755.20_summits.bed INFO @ Sat, 03 Apr 2021 07:20:06: Done! pass1 - making usageList (142 chroms): 1 millis pass2 - checking and writing primary data (1240 records, 4 fields): 6 millis CompletedMACS2peakCalling