Job ID = 12265305 SRX = SRX5010764 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 30566866 spots for SRR8191189/SRR8191189.sra Written 30566866 spots for SRR8191189/SRR8191189.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265461 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:08:01 30566866 reads; of these: 30566866 (100.00%) were unpaired; of these: 1438308 (4.71%) aligned 0 times 14821991 (48.49%) aligned exactly 1 time 14306567 (46.80%) aligned >1 times 95.29% overall alignment rate Time searching: 00:08:02 Overall time: 00:08:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 17219948 / 29128558 = 0.5912 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 06:45:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.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 06:45:37: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:45:37: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:45:43: 1000000 INFO @ Sat, 03 Apr 2021 06:45:48: 2000000 INFO @ Sat, 03 Apr 2021 06:45:53: 3000000 INFO @ Sat, 03 Apr 2021 06:45:59: 4000000 INFO @ Sat, 03 Apr 2021 06:46:04: 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 06:46:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.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 06:46:07: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:46:07: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:46:10: 6000000 INFO @ Sat, 03 Apr 2021 06:46:13: 1000000 INFO @ Sat, 03 Apr 2021 06:46:15: 7000000 INFO @ Sat, 03 Apr 2021 06:46:18: 2000000 INFO @ Sat, 03 Apr 2021 06:46:21: 8000000 INFO @ Sat, 03 Apr 2021 06:46:24: 3000000 INFO @ Sat, 03 Apr 2021 06:46:28: 9000000 INFO @ Sat, 03 Apr 2021 06:46:31: 4000000 INFO @ Sat, 03 Apr 2021 06:46:34: 10000000 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 06:46:36: 5000000 INFO @ Sat, 03 Apr 2021 06:46:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.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 06:46:37: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:46:37: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:46:40: 11000000 INFO @ Sat, 03 Apr 2021 06:46:43: 6000000 INFO @ Sat, 03 Apr 2021 06:46:43: 1000000 INFO @ Sat, 03 Apr 2021 06:46:46: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:46:46: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:46:46: #1 total tags in treatment: 11908610 INFO @ Sat, 03 Apr 2021 06:46:46: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:46:46: #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 06:46:46: #1 tags after filtering in treatment: 11908610 INFO @ Sat, 03 Apr 2021 06:46:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:46:46: #1 finished! INFO @ Sat, 03 Apr 2021 06:46:46: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:46:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:46:47: #2 number of paired peaks: 461 WARNING @ Sat, 03 Apr 2021 06:46:47: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Sat, 03 Apr 2021 06:46:47: start model_add_line... INFO @ Sat, 03 Apr 2021 06:46:47: start X-correlation... INFO @ Sat, 03 Apr 2021 06:46:47: end of X-cor INFO @ Sat, 03 Apr 2021 06:46:47: #2 finished! INFO @ Sat, 03 Apr 2021 06:46:47: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Apr 2021 06:46:47: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sat, 03 Apr 2021 06:46:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.05_model.r WARNING @ Sat, 03 Apr 2021 06:46:47: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:46:47: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sat, 03 Apr 2021 06:46:47: #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 06:46:47: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:46:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:46:49: 7000000 INFO @ Sat, 03 Apr 2021 06:46:49: 2000000 INFO @ Sat, 03 Apr 2021 06:46:55: 8000000 INFO @ Sat, 03 Apr 2021 06:46:55: 3000000 INFO @ Sat, 03 Apr 2021 06:47:01: 9000000 INFO @ Sat, 03 Apr 2021 06:47:01: 4000000 INFO @ Sat, 03 Apr 2021 06:47:07: 10000000 INFO @ Sat, 03 Apr 2021 06:47:07: 5000000 INFO @ Sat, 03 Apr 2021 06:47:09: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:47:13: 11000000 INFO @ Sat, 03 Apr 2021 06:47:13: 6000000 INFO @ Sat, 03 Apr 2021 06:47:18: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:47:18: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:47:18: #1 total tags in treatment: 11908610 INFO @ Sat, 03 Apr 2021 06:47:18: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:47:18: #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 06:47:18: #1 tags after filtering in treatment: 11908610 INFO @ Sat, 03 Apr 2021 06:47:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:47:18: #1 finished! INFO @ Sat, 03 Apr 2021 06:47:18: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:47:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:47:19: 7000000 INFO @ Sat, 03 Apr 2021 06:47:19: #2 number of paired peaks: 461 WARNING @ Sat, 03 Apr 2021 06:47:19: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Sat, 03 Apr 2021 06:47:19: start model_add_line... INFO @ Sat, 03 Apr 2021 06:47:19: start X-correlation... INFO @ Sat, 03 Apr 2021 06:47:19: end of X-cor INFO @ Sat, 03 Apr 2021 06:47:19: #2 finished! INFO @ Sat, 03 Apr 2021 06:47:19: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Apr 2021 06:47:19: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sat, 03 Apr 2021 06:47:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.10_model.r WARNING @ Sat, 03 Apr 2021 06:47:19: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:47:19: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sat, 03 Apr 2021 06:47:19: #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 06:47:19: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:47:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:47:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:47:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:47:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.05_summits.bed INFO @ Sat, 03 Apr 2021 06:47:22: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5691 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:47:24: 8000000 INFO @ Sat, 03 Apr 2021 06:47:30: 9000000 INFO @ Sat, 03 Apr 2021 06:47:35: 10000000 INFO @ Sat, 03 Apr 2021 06:47:41: 11000000 INFO @ Sat, 03 Apr 2021 06:47:41: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:47:45: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:47:45: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:47:45: #1 total tags in treatment: 11908610 INFO @ Sat, 03 Apr 2021 06:47:45: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:47:45: #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 06:47:46: #1 tags after filtering in treatment: 11908610 INFO @ Sat, 03 Apr 2021 06:47:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:47:46: #1 finished! INFO @ Sat, 03 Apr 2021 06:47:46: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:47:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:47:47: #2 number of paired peaks: 461 WARNING @ Sat, 03 Apr 2021 06:47:47: Fewer paired peaks (461) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 461 pairs to build model! INFO @ Sat, 03 Apr 2021 06:47:47: start model_add_line... INFO @ Sat, 03 Apr 2021 06:47:47: start X-correlation... INFO @ Sat, 03 Apr 2021 06:47:47: end of X-cor INFO @ Sat, 03 Apr 2021 06:47:47: #2 finished! INFO @ Sat, 03 Apr 2021 06:47:47: #2 predicted fragment length is 52 bps INFO @ Sat, 03 Apr 2021 06:47:47: #2 alternative fragment length(s) may be 4,52 bps INFO @ Sat, 03 Apr 2021 06:47:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.20_model.r WARNING @ Sat, 03 Apr 2021 06:47:47: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:47:47: #2 You may need to consider one of the other alternative d(s): 4,52 WARNING @ Sat, 03 Apr 2021 06:47:47: #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 06:47:47: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:47:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:47:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:47:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:47:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.10_summits.bed INFO @ Sat, 03 Apr 2021 06:47:54: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2483 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:48:09: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:48:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:48:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:48:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010764/SRX5010764.20_summits.bed INFO @ Sat, 03 Apr 2021 06:48:21: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (409 records, 4 fields): 3 millis CompletedMACS2peakCalling