Job ID = 12265301 SRX = SRX5010760 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 31521343 spots for SRR8191185/SRR8191185.sra Written 31521343 spots for SRR8191185/SRR8191185.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265452 ("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: 00:08:41 31521343 reads; of these: 31521343 (100.00%) were unpaired; of these: 949592 (3.01%) aligned 0 times 14191852 (45.02%) aligned exactly 1 time 16379899 (51.96%) aligned >1 times 96.99% overall alignment rate Time searching: 00:08:41 Overall time: 00:08:41 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 16 files... [bam_rmdupse_core] 16665090 / 30571751 = 0.5451 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 06:43:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.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 06:43:06: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:43:06: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:43:11: 1000000 INFO @ Sat, 03 Apr 2021 06:43:16: 2000000 INFO @ Sat, 03 Apr 2021 06:43:21: 3000000 INFO @ Sat, 03 Apr 2021 06:43:26: 4000000 INFO @ Sat, 03 Apr 2021 06:43:31: 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 06:43:36: 6000000 INFO @ Sat, 03 Apr 2021 06:43:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.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 06:43:36: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:43:36: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:43:41: 7000000 INFO @ Sat, 03 Apr 2021 06:43:41: 1000000 INFO @ Sat, 03 Apr 2021 06:43:46: 8000000 INFO @ Sat, 03 Apr 2021 06:43:46: 2000000 INFO @ Sat, 03 Apr 2021 06:43:51: 9000000 INFO @ Sat, 03 Apr 2021 06:43:51: 3000000 INFO @ Sat, 03 Apr 2021 06:43:57: 10000000 INFO @ Sat, 03 Apr 2021 06:43:57: 4000000 INFO @ Sat, 03 Apr 2021 06:44:02: 11000000 INFO @ Sat, 03 Apr 2021 06:44:02: 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 06:44:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.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 06:44:06: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:44:06: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:44:07: 12000000 INFO @ Sat, 03 Apr 2021 06:44:07: 6000000 INFO @ Sat, 03 Apr 2021 06:44:11: 1000000 INFO @ Sat, 03 Apr 2021 06:44:12: 7000000 INFO @ Sat, 03 Apr 2021 06:44:12: 13000000 INFO @ Sat, 03 Apr 2021 06:44:17: 2000000 INFO @ Sat, 03 Apr 2021 06:44:17: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:44:17: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:44:17: #1 total tags in treatment: 13906661 INFO @ Sat, 03 Apr 2021 06:44:17: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:44:17: #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 06:44:18: #1 tags after filtering in treatment: 13906661 INFO @ Sat, 03 Apr 2021 06:44:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:44:18: #1 finished! INFO @ Sat, 03 Apr 2021 06:44:18: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:44:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:44:18: 8000000 INFO @ Sat, 03 Apr 2021 06:44:19: #2 number of paired peaks: 130 WARNING @ Sat, 03 Apr 2021 06:44:19: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Sat, 03 Apr 2021 06:44:19: start model_add_line... INFO @ Sat, 03 Apr 2021 06:44:19: start X-correlation... INFO @ Sat, 03 Apr 2021 06:44:19: end of X-cor INFO @ Sat, 03 Apr 2021 06:44:19: #2 finished! INFO @ Sat, 03 Apr 2021 06:44:19: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Apr 2021 06:44:19: #2 alternative fragment length(s) may be 3,49,507,543 bps INFO @ Sat, 03 Apr 2021 06:44:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.05_model.r WARNING @ Sat, 03 Apr 2021 06:44:19: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:44:19: #2 You may need to consider one of the other alternative d(s): 3,49,507,543 WARNING @ Sat, 03 Apr 2021 06:44:19: #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 06:44:19: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:44:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:44:22: 3000000 INFO @ Sat, 03 Apr 2021 06:44:23: 9000000 INFO @ Sat, 03 Apr 2021 06:44:27: 4000000 INFO @ Sat, 03 Apr 2021 06:44:28: 10000000 INFO @ Sat, 03 Apr 2021 06:44:32: 5000000 INFO @ Sat, 03 Apr 2021 06:44:33: 11000000 INFO @ Sat, 03 Apr 2021 06:44:38: 6000000 INFO @ Sat, 03 Apr 2021 06:44:39: 12000000 INFO @ Sat, 03 Apr 2021 06:44:43: 7000000 INFO @ Sat, 03 Apr 2021 06:44:44: 13000000 INFO @ Sat, 03 Apr 2021 06:44:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:44:48: 8000000 INFO @ Sat, 03 Apr 2021 06:44:49: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:44:49: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:44:49: #1 total tags in treatment: 13906661 INFO @ Sat, 03 Apr 2021 06:44:49: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:44:49: #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 06:44:49: #1 tags after filtering in treatment: 13906661 INFO @ Sat, 03 Apr 2021 06:44:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:44:49: #1 finished! INFO @ Sat, 03 Apr 2021 06:44:49: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:44:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:44:50: #2 number of paired peaks: 130 WARNING @ Sat, 03 Apr 2021 06:44:50: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Sat, 03 Apr 2021 06:44:50: start model_add_line... INFO @ Sat, 03 Apr 2021 06:44:50: start X-correlation... INFO @ Sat, 03 Apr 2021 06:44:50: end of X-cor INFO @ Sat, 03 Apr 2021 06:44:50: #2 finished! INFO @ Sat, 03 Apr 2021 06:44:50: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Apr 2021 06:44:50: #2 alternative fragment length(s) may be 3,49,507,543 bps INFO @ Sat, 03 Apr 2021 06:44:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.10_model.r WARNING @ Sat, 03 Apr 2021 06:44:50: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:44:50: #2 You may need to consider one of the other alternative d(s): 3,49,507,543 WARNING @ Sat, 03 Apr 2021 06:44:50: #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 06:44:50: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:44:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:44:54: 9000000 INFO @ Sat, 03 Apr 2021 06:44:59: 10000000 INFO @ Sat, 03 Apr 2021 06:45:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:45:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:45:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.05_summits.bed INFO @ Sat, 03 Apr 2021 06:45:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3341 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:45:04: 11000000 INFO @ Sat, 03 Apr 2021 06:45:09: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:45:14: 13000000 INFO @ Sat, 03 Apr 2021 06:45:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:45:18: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:45:18: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:45:18: #1 total tags in treatment: 13906661 INFO @ Sat, 03 Apr 2021 06:45:18: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:45:18: #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 06:45:19: #1 tags after filtering in treatment: 13906661 INFO @ Sat, 03 Apr 2021 06:45:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:45:19: #1 finished! INFO @ Sat, 03 Apr 2021 06:45:19: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:45:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:45:19: #2 number of paired peaks: 130 WARNING @ Sat, 03 Apr 2021 06:45:19: Fewer paired peaks (130) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 130 pairs to build model! INFO @ Sat, 03 Apr 2021 06:45:19: start model_add_line... INFO @ Sat, 03 Apr 2021 06:45:20: start X-correlation... INFO @ Sat, 03 Apr 2021 06:45:20: end of X-cor INFO @ Sat, 03 Apr 2021 06:45:20: #2 finished! INFO @ Sat, 03 Apr 2021 06:45:20: #2 predicted fragment length is 49 bps INFO @ Sat, 03 Apr 2021 06:45:20: #2 alternative fragment length(s) may be 3,49,507,543 bps INFO @ Sat, 03 Apr 2021 06:45:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.20_model.r WARNING @ Sat, 03 Apr 2021 06:45:20: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:45:20: #2 You may need to consider one of the other alternative d(s): 3,49,507,543 WARNING @ Sat, 03 Apr 2021 06:45:20: #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 06:45:20: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:45:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:45:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:45:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:45:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.10_summits.bed INFO @ Sat, 03 Apr 2021 06:45:32: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1246 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:45:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:46:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:46:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:46:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010760/SRX5010760.20_summits.bed INFO @ Sat, 03 Apr 2021 06:46:02: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (138 records, 4 fields): 1 millis CompletedMACS2peakCalling