Job ID = 14170553 SRX = SRX9720889 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9619195 spots for SRR13291879/SRR13291879.sra Written 9619195 spots for SRR13291879/SRR13291879.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170950 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:12 9619195 reads; of these: 9619195 (100.00%) were unpaired; of these: 485478 (5.05%) aligned 0 times 5963385 (61.99%) aligned exactly 1 time 3170332 (32.96%) aligned >1 times 94.95% overall alignment rate Time searching: 00:03:12 Overall time: 00:03:12 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_rmdupse_core] 784718 / 9133717 = 0.0859 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 @ Sat, 11 Dec 2021 07:17:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.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, 11 Dec 2021 07:17:13: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:17:13: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:17:18: 1000000 INFO @ Sat, 11 Dec 2021 07:17:23: 2000000 INFO @ Sat, 11 Dec 2021 07:17:28: 3000000 INFO @ Sat, 11 Dec 2021 07:17:33: 4000000 INFO @ Sat, 11 Dec 2021 07:17:39: 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 @ Sat, 11 Dec 2021 07:17:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.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, 11 Dec 2021 07:17:41: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:17:41: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:17:44: 6000000 INFO @ Sat, 11 Dec 2021 07:17:46: 1000000 INFO @ Sat, 11 Dec 2021 07:17:50: 7000000 INFO @ Sat, 11 Dec 2021 07:17:52: 2000000 INFO @ Sat, 11 Dec 2021 07:17:55: 8000000 INFO @ Sat, 11 Dec 2021 07:17:57: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:17:57: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:17:57: #1 total tags in treatment: 8348999 INFO @ Sat, 11 Dec 2021 07:17:57: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:17:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:17:57: #1 tags after filtering in treatment: 8348999 INFO @ Sat, 11 Dec 2021 07:17:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:17:57: #1 finished! INFO @ Sat, 11 Dec 2021 07:17:57: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:17:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:17:58: 3000000 INFO @ Sat, 11 Dec 2021 07:17:58: #2 number of paired peaks: 667 WARNING @ Sat, 11 Dec 2021 07:17:58: Fewer paired peaks (667) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 667 pairs to build model! INFO @ Sat, 11 Dec 2021 07:17:58: start model_add_line... INFO @ Sat, 11 Dec 2021 07:17:58: start X-correlation... INFO @ Sat, 11 Dec 2021 07:17:58: end of X-cor INFO @ Sat, 11 Dec 2021 07:17:58: #2 finished! INFO @ Sat, 11 Dec 2021 07:17:58: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 07:17:58: #2 alternative fragment length(s) may be 4,52,558 bps INFO @ Sat, 11 Dec 2021 07:17:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.05_model.r WARNING @ Sat, 11 Dec 2021 07:17:58: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:17:58: #2 You may need to consider one of the other alternative d(s): 4,52,558 WARNING @ Sat, 11 Dec 2021 07:17:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:17:58: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:17:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:18:03: 4000000 INFO @ Sat, 11 Dec 2021 07:18:09: 5000000 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 @ Sat, 11 Dec 2021 07:18:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.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, 11 Dec 2021 07:18:11: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:18:11: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:18:14: 6000000 INFO @ Sat, 11 Dec 2021 07:18:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:18:16: 1000000 INFO @ Sat, 11 Dec 2021 07:18:20: 7000000 INFO @ Sat, 11 Dec 2021 07:18:22: 2000000 INFO @ Sat, 11 Dec 2021 07:18:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:18:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:18:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.05_summits.bed INFO @ Sat, 11 Dec 2021 07:18:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2578 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:18:25: 8000000 INFO @ Sat, 11 Dec 2021 07:18:27: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:18:27: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:18:27: #1 total tags in treatment: 8348999 INFO @ Sat, 11 Dec 2021 07:18:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:18:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:18:27: #1 tags after filtering in treatment: 8348999 INFO @ Sat, 11 Dec 2021 07:18:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:18:27: #1 finished! INFO @ Sat, 11 Dec 2021 07:18:27: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:18:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:18:28: 3000000 INFO @ Sat, 11 Dec 2021 07:18:28: #2 number of paired peaks: 667 WARNING @ Sat, 11 Dec 2021 07:18:28: Fewer paired peaks (667) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 667 pairs to build model! INFO @ Sat, 11 Dec 2021 07:18:28: start model_add_line... INFO @ Sat, 11 Dec 2021 07:18:28: start X-correlation... INFO @ Sat, 11 Dec 2021 07:18:28: end of X-cor INFO @ Sat, 11 Dec 2021 07:18:28: #2 finished! INFO @ Sat, 11 Dec 2021 07:18:28: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 07:18:28: #2 alternative fragment length(s) may be 4,52,558 bps INFO @ Sat, 11 Dec 2021 07:18:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.10_model.r WARNING @ Sat, 11 Dec 2021 07:18:28: #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, 11 Dec 2021 07:18:28: #2 You may need to consider one of the other alternative d(s): 4,52,558 WARNING @ Sat, 11 Dec 2021 07:18:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:18:28: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:18:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:18:33: 4000000 INFO @ Sat, 11 Dec 2021 07:18:38: 5000000 INFO @ Sat, 11 Dec 2021 07:18:43: 6000000 INFO @ Sat, 11 Dec 2021 07:18:44: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:18:49: 7000000 INFO @ Sat, 11 Dec 2021 07:18:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:18:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:18:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.10_summits.bed INFO @ Sat, 11 Dec 2021 07:18:53: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1448 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:18:54: 8000000 INFO @ Sat, 11 Dec 2021 07:18:56: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:18:56: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:18:56: #1 total tags in treatment: 8348999 INFO @ Sat, 11 Dec 2021 07:18:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:18:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 07:18:56: #1 tags after filtering in treatment: 8348999 INFO @ Sat, 11 Dec 2021 07:18:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:18:56: #1 finished! INFO @ Sat, 11 Dec 2021 07:18:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:18:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:18:56: #2 number of paired peaks: 667 WARNING @ Sat, 11 Dec 2021 07:18:56: Fewer paired peaks (667) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 667 pairs to build model! INFO @ Sat, 11 Dec 2021 07:18:56: start model_add_line... INFO @ Sat, 11 Dec 2021 07:18:56: start X-correlation... INFO @ Sat, 11 Dec 2021 07:18:56: end of X-cor INFO @ Sat, 11 Dec 2021 07:18:56: #2 finished! INFO @ Sat, 11 Dec 2021 07:18:56: #2 predicted fragment length is 52 bps INFO @ Sat, 11 Dec 2021 07:18:56: #2 alternative fragment length(s) may be 4,52,558 bps INFO @ Sat, 11 Dec 2021 07:18:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.20_model.r WARNING @ Sat, 11 Dec 2021 07:18:56: #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, 11 Dec 2021 07:18:56: #2 You may need to consider one of the other alternative d(s): 4,52,558 WARNING @ Sat, 11 Dec 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, 11 Dec 2021 07:18:56: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:18:56: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:19:12: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:19:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:19:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:19:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720889/SRX9720889.20_summits.bed INFO @ Sat, 11 Dec 2021 07:19:21: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (445 records, 4 fields): 1 millis CompletedMACS2peakCalling