Job ID = 12265308 SRX = SRX5010767 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 31491896 spots for SRR8191192/SRR8191192.sra Written 31491896 spots for SRR8191192/SRR8191192.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265495 ("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: 00:13:10 31491896 reads; of these: 31491896 (100.00%) were unpaired; of these: 1826716 (5.80%) aligned 0 times 14960117 (47.50%) aligned exactly 1 time 14705063 (46.69%) aligned >1 times 94.20% overall alignment rate Time searching: 00:13:10 Overall time: 00:13:10 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] 16608807 / 29665180 = 0.5599 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 06:54:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.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 06:54:04: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:54:04: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:54:15: 1000000 INFO @ Sat, 03 Apr 2021 06:54:27: 2000000 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 06:54:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.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 06:54:34: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:54:34: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:54:39: 3000000 INFO @ Sat, 03 Apr 2021 06:54:49: 1000000 INFO @ Sat, 03 Apr 2021 06:54:54: 4000000 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 06:55:04: 2000000 INFO @ Sat, 03 Apr 2021 06:55:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.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 06:55:04: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:55:04: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:55:09: 5000000 INFO @ Sat, 03 Apr 2021 06:55:14: 1000000 INFO @ Sat, 03 Apr 2021 06:55:19: 3000000 INFO @ Sat, 03 Apr 2021 06:55:23: 6000000 INFO @ Sat, 03 Apr 2021 06:55:24: 2000000 INFO @ Sat, 03 Apr 2021 06:55:33: 3000000 INFO @ Sat, 03 Apr 2021 06:55:34: 4000000 INFO @ Sat, 03 Apr 2021 06:55:38: 7000000 INFO @ Sat, 03 Apr 2021 06:55:43: 4000000 INFO @ Sat, 03 Apr 2021 06:55:48: 5000000 INFO @ Sat, 03 Apr 2021 06:55:53: 8000000 INFO @ Sat, 03 Apr 2021 06:55:54: 5000000 INFO @ Sat, 03 Apr 2021 06:56:03: 6000000 INFO @ Sat, 03 Apr 2021 06:56:03: 6000000 INFO @ Sat, 03 Apr 2021 06:56:08: 9000000 INFO @ Sat, 03 Apr 2021 06:56:13: 7000000 INFO @ Sat, 03 Apr 2021 06:56:18: 7000000 INFO @ Sat, 03 Apr 2021 06:56:23: 8000000 INFO @ Sat, 03 Apr 2021 06:56:24: 10000000 INFO @ Sat, 03 Apr 2021 06:56:32: 8000000 INFO @ Sat, 03 Apr 2021 06:56:32: 9000000 INFO @ Sat, 03 Apr 2021 06:56:39: 11000000 INFO @ Sat, 03 Apr 2021 06:56:43: 10000000 INFO @ Sat, 03 Apr 2021 06:56:45: 9000000 INFO @ Sat, 03 Apr 2021 06:56:54: 12000000 INFO @ Sat, 03 Apr 2021 06:56:54: 11000000 INFO @ Sat, 03 Apr 2021 06:57:01: 10000000 INFO @ Sat, 03 Apr 2021 06:57:03: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:57:08: 13000000 INFO @ Sat, 03 Apr 2021 06:57:09: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:57:09: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:57:09: #1 total tags in treatment: 13056373 INFO @ Sat, 03 Apr 2021 06:57:09: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:57:09: #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 06:57:09: #1 tags after filtering in treatment: 13056373 INFO @ Sat, 03 Apr 2021 06:57:09: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:57:09: #1 finished! INFO @ Sat, 03 Apr 2021 06:57:09: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:57:09: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:57:10: #2 number of paired peaks: 202 WARNING @ Sat, 03 Apr 2021 06:57:10: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Sat, 03 Apr 2021 06:57:10: start model_add_line... INFO @ Sat, 03 Apr 2021 06:57:10: start X-correlation... INFO @ Sat, 03 Apr 2021 06:57:10: end of X-cor INFO @ Sat, 03 Apr 2021 06:57:10: #2 finished! INFO @ Sat, 03 Apr 2021 06:57:10: #2 predicted fragment length is 43 bps INFO @ Sat, 03 Apr 2021 06:57:10: #2 alternative fragment length(s) may be 3,43 bps INFO @ Sat, 03 Apr 2021 06:57:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.05_model.r WARNING @ Sat, 03 Apr 2021 06:57:10: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:57:10: #2 You may need to consider one of the other alternative d(s): 3,43 WARNING @ Sat, 03 Apr 2021 06:57:10: #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 06:57:10: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:57:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:57:14: 13000000 INFO @ Sat, 03 Apr 2021 06:57:14: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:57:14: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:57:14: #1 total tags in treatment: 13056373 INFO @ Sat, 03 Apr 2021 06:57:14: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:57:14: #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 06:57:15: 11000000 INFO @ Sat, 03 Apr 2021 06:57:15: #1 tags after filtering in treatment: 13056373 INFO @ Sat, 03 Apr 2021 06:57:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:57:15: #1 finished! INFO @ Sat, 03 Apr 2021 06:57:15: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:57:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:57:16: #2 number of paired peaks: 202 WARNING @ Sat, 03 Apr 2021 06:57:16: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Sat, 03 Apr 2021 06:57:16: start model_add_line... INFO @ Sat, 03 Apr 2021 06:57:16: start X-correlation... INFO @ Sat, 03 Apr 2021 06:57:16: end of X-cor INFO @ Sat, 03 Apr 2021 06:57:16: #2 finished! INFO @ Sat, 03 Apr 2021 06:57:16: #2 predicted fragment length is 43 bps INFO @ Sat, 03 Apr 2021 06:57:16: #2 alternative fragment length(s) may be 3,43 bps INFO @ Sat, 03 Apr 2021 06:57:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.20_model.r WARNING @ Sat, 03 Apr 2021 06:57:16: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:57:16: #2 You may need to consider one of the other alternative d(s): 3,43 WARNING @ Sat, 03 Apr 2021 06:57:16: #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 06:57:16: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:57:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:57:27: 12000000 INFO @ Sat, 03 Apr 2021 06:57:37: 13000000 INFO @ Sat, 03 Apr 2021 06:57:38: #1 tag size is determined as 50 bps INFO @ Sat, 03 Apr 2021 06:57:38: #1 tag size = 50 INFO @ Sat, 03 Apr 2021 06:57:38: #1 total tags in treatment: 13056373 INFO @ Sat, 03 Apr 2021 06:57:38: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:57:38: #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 06:57:38: #1 tags after filtering in treatment: 13056373 INFO @ Sat, 03 Apr 2021 06:57:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:57:38: #1 finished! INFO @ Sat, 03 Apr 2021 06:57:38: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:57:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:57:40: #2 number of paired peaks: 202 WARNING @ Sat, 03 Apr 2021 06:57:40: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Sat, 03 Apr 2021 06:57:40: start model_add_line... INFO @ Sat, 03 Apr 2021 06:57:40: start X-correlation... INFO @ Sat, 03 Apr 2021 06:57:40: end of X-cor INFO @ Sat, 03 Apr 2021 06:57:40: #2 finished! INFO @ Sat, 03 Apr 2021 06:57:40: #2 predicted fragment length is 43 bps INFO @ Sat, 03 Apr 2021 06:57:40: #2 alternative fragment length(s) may be 3,43 bps INFO @ Sat, 03 Apr 2021 06:57:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.10_model.r WARNING @ Sat, 03 Apr 2021 06:57:40: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:57:40: #2 You may need to consider one of the other alternative d(s): 3,43 WARNING @ Sat, 03 Apr 2021 06:57:40: #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 06:57:40: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:57:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:57:49: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:57:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:58:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:58:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:58:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.05_summits.bed INFO @ Sat, 03 Apr 2021 06:58:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3736 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:58:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:58:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:58:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.20_summits.bed INFO @ Sat, 03 Apr 2021 06:58:14: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (147 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:58:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:58:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:58:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:58:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5010767/SRX5010767.10_summits.bed INFO @ Sat, 03 Apr 2021 06:58:37: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1469 records, 4 fields): 7 millis CompletedMACS2peakCalling