Job ID = 14170375 SRX = SRX9720910 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21641613 spots for SRR13291900/SRR13291900.sra Written 21641613 spots for SRR13291900/SRR13291900.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170774 ("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: 00:07:31 21641613 reads; of these: 21641613 (100.00%) were unpaired; of these: 830634 (3.84%) aligned 0 times 14414773 (66.61%) aligned exactly 1 time 6396206 (29.56%) aligned >1 times 96.16% overall alignment rate Time searching: 00:07:31 Overall time: 00:07:31 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] 2005977 / 20810979 = 0.0964 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 06:38:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.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 06:38:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:38:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:38:11: 1000000 INFO @ Sat, 11 Dec 2021 06:38:16: 2000000 INFO @ Sat, 11 Dec 2021 06:38:21: 3000000 INFO @ Sat, 11 Dec 2021 06:38:26: 4000000 INFO @ Sat, 11 Dec 2021 06:38:31: 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 06:38:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.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 06:38:36: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:38:36: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:38:37: 6000000 INFO @ Sat, 11 Dec 2021 06:38:43: 7000000 INFO @ Sat, 11 Dec 2021 06:38:43: 1000000 INFO @ Sat, 11 Dec 2021 06:38:49: 8000000 INFO @ Sat, 11 Dec 2021 06:38:50: 2000000 INFO @ Sat, 11 Dec 2021 06:38:54: 9000000 INFO @ Sat, 11 Dec 2021 06:38:57: 3000000 INFO @ Sat, 11 Dec 2021 06:39:00: 10000000 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 06:39:04: 4000000 INFO @ Sat, 11 Dec 2021 06:39:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.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 06:39:06: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:39:06: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:39:06: 11000000 INFO @ Sat, 11 Dec 2021 06:39:11: 5000000 INFO @ Sat, 11 Dec 2021 06:39:12: 1000000 INFO @ Sat, 11 Dec 2021 06:39:12: 12000000 INFO @ Sat, 11 Dec 2021 06:39:18: 6000000 INFO @ Sat, 11 Dec 2021 06:39:18: 13000000 INFO @ Sat, 11 Dec 2021 06:39:19: 2000000 INFO @ Sat, 11 Dec 2021 06:39:25: 14000000 INFO @ Sat, 11 Dec 2021 06:39:25: 3000000 INFO @ Sat, 11 Dec 2021 06:39:25: 7000000 INFO @ Sat, 11 Dec 2021 06:39:31: 15000000 INFO @ Sat, 11 Dec 2021 06:39:31: 4000000 INFO @ Sat, 11 Dec 2021 06:39:32: 8000000 INFO @ Sat, 11 Dec 2021 06:39:37: 16000000 INFO @ Sat, 11 Dec 2021 06:39:37: 5000000 INFO @ Sat, 11 Dec 2021 06:39:39: 9000000 INFO @ Sat, 11 Dec 2021 06:39:43: 17000000 INFO @ Sat, 11 Dec 2021 06:39:43: 6000000 INFO @ Sat, 11 Dec 2021 06:39:46: 10000000 INFO @ Sat, 11 Dec 2021 06:39:49: 18000000 INFO @ Sat, 11 Dec 2021 06:39:49: 7000000 INFO @ Sat, 11 Dec 2021 06:39:53: 11000000 INFO @ Sat, 11 Dec 2021 06:39:54: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:39:54: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:39:54: #1 total tags in treatment: 18805002 INFO @ Sat, 11 Dec 2021 06:39:54: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:39:54: #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 06:39:54: #1 tags after filtering in treatment: 18805002 INFO @ Sat, 11 Dec 2021 06:39:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:39:54: #1 finished! INFO @ Sat, 11 Dec 2021 06:39:54: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:39:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:39:55: #2 number of paired peaks: 356 WARNING @ Sat, 11 Dec 2021 06:39:55: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Sat, 11 Dec 2021 06:39:55: start model_add_line... INFO @ Sat, 11 Dec 2021 06:39:55: start X-correlation... INFO @ Sat, 11 Dec 2021 06:39:55: end of X-cor INFO @ Sat, 11 Dec 2021 06:39:55: #2 finished! INFO @ Sat, 11 Dec 2021 06:39:55: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Dec 2021 06:39:55: #2 alternative fragment length(s) may be 3,57 bps INFO @ Sat, 11 Dec 2021 06:39:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.05_model.r WARNING @ Sat, 11 Dec 2021 06:39:55: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:39:55: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Sat, 11 Dec 2021 06:39:55: #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 06:39:55: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:39:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:39:56: 8000000 INFO @ Sat, 11 Dec 2021 06:40:00: 12000000 INFO @ Sat, 11 Dec 2021 06:40:02: 9000000 INFO @ Sat, 11 Dec 2021 06:40:07: 13000000 INFO @ Sat, 11 Dec 2021 06:40:08: 10000000 INFO @ Sat, 11 Dec 2021 06:40:13: 11000000 INFO @ Sat, 11 Dec 2021 06:40:14: 14000000 INFO @ Sat, 11 Dec 2021 06:40:19: 12000000 INFO @ Sat, 11 Dec 2021 06:40:21: 15000000 INFO @ Sat, 11 Dec 2021 06:40:25: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:40:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:40:27: 16000000 INFO @ Sat, 11 Dec 2021 06:40:31: 14000000 INFO @ Sat, 11 Dec 2021 06:40:34: 17000000 INFO @ Sat, 11 Dec 2021 06:40:37: 15000000 INFO @ Sat, 11 Dec 2021 06:40:41: 18000000 INFO @ Sat, 11 Dec 2021 06:40:43: 16000000 INFO @ Sat, 11 Dec 2021 06:40:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:40:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:40:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.05_summits.bed INFO @ Sat, 11 Dec 2021 06:40:43: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3830 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:40:46: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:40:46: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:40:46: #1 total tags in treatment: 18805002 INFO @ Sat, 11 Dec 2021 06:40:46: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:40:46: #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 06:40:47: #1 tags after filtering in treatment: 18805002 INFO @ Sat, 11 Dec 2021 06:40:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:40:47: #1 finished! INFO @ Sat, 11 Dec 2021 06:40:47: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:40:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:40:48: #2 number of paired peaks: 356 WARNING @ Sat, 11 Dec 2021 06:40:48: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Sat, 11 Dec 2021 06:40:48: start model_add_line... INFO @ Sat, 11 Dec 2021 06:40:48: start X-correlation... INFO @ Sat, 11 Dec 2021 06:40:48: end of X-cor INFO @ Sat, 11 Dec 2021 06:40:48: #2 finished! INFO @ Sat, 11 Dec 2021 06:40:48: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Dec 2021 06:40:48: #2 alternative fragment length(s) may be 3,57 bps INFO @ Sat, 11 Dec 2021 06:40:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.10_model.r WARNING @ Sat, 11 Dec 2021 06:40:48: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:40:48: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Sat, 11 Dec 2021 06:40:48: #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 06:40:48: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:40:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:40:49: 17000000 INFO @ Sat, 11 Dec 2021 06:40:54: 18000000 INFO @ Sat, 11 Dec 2021 06:40:58: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:40:58: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:40:58: #1 total tags in treatment: 18805002 INFO @ Sat, 11 Dec 2021 06:40:58: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:40:58: #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 06:40:59: #1 tags after filtering in treatment: 18805002 INFO @ Sat, 11 Dec 2021 06:40:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:40:59: #1 finished! INFO @ Sat, 11 Dec 2021 06:40:59: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:40:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:41:00: #2 number of paired peaks: 356 WARNING @ Sat, 11 Dec 2021 06:41:00: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Sat, 11 Dec 2021 06:41:00: start model_add_line... INFO @ Sat, 11 Dec 2021 06:41:00: start X-correlation... INFO @ Sat, 11 Dec 2021 06:41:00: end of X-cor INFO @ Sat, 11 Dec 2021 06:41:00: #2 finished! INFO @ Sat, 11 Dec 2021 06:41:00: #2 predicted fragment length is 57 bps INFO @ Sat, 11 Dec 2021 06:41:00: #2 alternative fragment length(s) may be 3,57 bps INFO @ Sat, 11 Dec 2021 06:41:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.20_model.r WARNING @ Sat, 11 Dec 2021 06:41:00: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:41:00: #2 You may need to consider one of the other alternative d(s): 3,57 WARNING @ Sat, 11 Dec 2021 06:41:00: #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 06:41:00: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:41:00: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:41:21: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:41:32: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:41:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:41:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:41:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.10_summits.bed INFO @ Sat, 11 Dec 2021 06:41:39: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2331 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:41:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:41:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:41:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720910/SRX9720910.20_summits.bed INFO @ Sat, 11 Dec 2021 06:41:49: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (730 records, 4 fields): 16 millis CompletedMACS2peakCalling