Job ID = 14170481 SRX = SRX8689042 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 17797151 spots for SRR12174242/SRR12174242.sra Written 17797151 spots for SRR12174242/SRR12174242.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170906 ("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: 00:06:28 17797151 reads; of these: 17797151 (100.00%) were unpaired; of these: 581150 (3.27%) aligned 0 times 11445100 (64.31%) aligned exactly 1 time 5770901 (32.43%) aligned >1 times 96.73% overall alignment rate Time searching: 00:06:28 Overall time: 00:06:28 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 8 files... [bam_rmdupse_core] 1637529 / 17216001 = 0.0951 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 07:05:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.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 07:05:53: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:05:53: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:05:59: 1000000 INFO @ Sat, 11 Dec 2021 07:06:05: 2000000 INFO @ Sat, 11 Dec 2021 07:06:11: 3000000 INFO @ Sat, 11 Dec 2021 07:06:16: 4000000 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 07:06:22: 5000000 INFO @ Sat, 11 Dec 2021 07:06:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.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 07:06:23: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:06:23: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:06:28: 6000000 INFO @ Sat, 11 Dec 2021 07:06:29: 1000000 INFO @ Sat, 11 Dec 2021 07:06:34: 7000000 INFO @ Sat, 11 Dec 2021 07:06:36: 2000000 INFO @ Sat, 11 Dec 2021 07:06:41: 8000000 INFO @ Sat, 11 Dec 2021 07:06:42: 3000000 INFO @ Sat, 11 Dec 2021 07:06:47: 9000000 INFO @ Sat, 11 Dec 2021 07:06:48: 4000000 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 07:06:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.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 07:06:53: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:06:53: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:06:53: 10000000 INFO @ Sat, 11 Dec 2021 07:06:55: 5000000 INFO @ Sat, 11 Dec 2021 07:07:00: 11000000 INFO @ Sat, 11 Dec 2021 07:07:00: 1000000 INFO @ Sat, 11 Dec 2021 07:07:02: 6000000 INFO @ Sat, 11 Dec 2021 07:07:07: 12000000 INFO @ Sat, 11 Dec 2021 07:07:08: 2000000 INFO @ Sat, 11 Dec 2021 07:07:09: 7000000 INFO @ Sat, 11 Dec 2021 07:07:14: 13000000 INFO @ Sat, 11 Dec 2021 07:07:16: 8000000 INFO @ Sat, 11 Dec 2021 07:07:16: 3000000 INFO @ Sat, 11 Dec 2021 07:07:21: 14000000 INFO @ Sat, 11 Dec 2021 07:07:22: 9000000 INFO @ Sat, 11 Dec 2021 07:07:24: 4000000 INFO @ Sat, 11 Dec 2021 07:07:28: 15000000 INFO @ Sat, 11 Dec 2021 07:07:29: 10000000 INFO @ Sat, 11 Dec 2021 07:07:31: 5000000 INFO @ Sat, 11 Dec 2021 07:07:32: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:07:32: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:07:32: #1 total tags in treatment: 15578472 INFO @ Sat, 11 Dec 2021 07:07:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:07:32: #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 07:07:32: #1 tags after filtering in treatment: 15578472 INFO @ Sat, 11 Dec 2021 07:07:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:07:32: #1 finished! INFO @ Sat, 11 Dec 2021 07:07:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:07:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:07:33: #2 number of paired peaks: 156 WARNING @ Sat, 11 Dec 2021 07:07:33: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Sat, 11 Dec 2021 07:07:33: start model_add_line... INFO @ Sat, 11 Dec 2021 07:07:33: start X-correlation... INFO @ Sat, 11 Dec 2021 07:07:33: end of X-cor INFO @ Sat, 11 Dec 2021 07:07:33: #2 finished! INFO @ Sat, 11 Dec 2021 07:07:33: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 07:07:33: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 11 Dec 2021 07:07:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.05_model.r WARNING @ Sat, 11 Dec 2021 07:07:33: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:07:33: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 11 Dec 2021 07:07:33: #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 07:07:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:07:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:07:36: 11000000 INFO @ Sat, 11 Dec 2021 07:07:39: 6000000 INFO @ Sat, 11 Dec 2021 07:07:43: 12000000 INFO @ Sat, 11 Dec 2021 07:07:46: 7000000 INFO @ Sat, 11 Dec 2021 07:07:50: 13000000 INFO @ Sat, 11 Dec 2021 07:07:54: 8000000 INFO @ Sat, 11 Dec 2021 07:07:57: 14000000 INFO @ Sat, 11 Dec 2021 07:08:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:08:01: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:08:04: 15000000 INFO @ Sat, 11 Dec 2021 07:08:08: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:08:08: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:08:08: #1 total tags in treatment: 15578472 INFO @ Sat, 11 Dec 2021 07:08:08: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:08:08: #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 07:08:08: #1 tags after filtering in treatment: 15578472 INFO @ Sat, 11 Dec 2021 07:08:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:08:08: #1 finished! INFO @ Sat, 11 Dec 2021 07:08:08: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:08:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:08:09: 10000000 INFO @ Sat, 11 Dec 2021 07:08:09: #2 number of paired peaks: 156 WARNING @ Sat, 11 Dec 2021 07:08:09: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Sat, 11 Dec 2021 07:08:09: start model_add_line... INFO @ Sat, 11 Dec 2021 07:08:09: start X-correlation... INFO @ Sat, 11 Dec 2021 07:08:09: end of X-cor INFO @ Sat, 11 Dec 2021 07:08:09: #2 finished! INFO @ Sat, 11 Dec 2021 07:08:09: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 07:08:09: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 11 Dec 2021 07:08:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.10_model.r WARNING @ Sat, 11 Dec 2021 07:08:09: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:08:09: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 11 Dec 2021 07:08:09: #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 07:08:09: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:08:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:08:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:08:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:08:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.05_summits.bed INFO @ Sat, 11 Dec 2021 07:08:15: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1983 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:08:16: 11000000 INFO @ Sat, 11 Dec 2021 07:08:23: 12000000 INFO @ Sat, 11 Dec 2021 07:08:30: 13000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:08:37: 14000000 INFO @ Sat, 11 Dec 2021 07:08:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:08:44: 15000000 INFO @ Sat, 11 Dec 2021 07:08:48: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:08:48: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:08:48: #1 total tags in treatment: 15578472 INFO @ Sat, 11 Dec 2021 07:08:48: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:08:48: #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 07:08:49: #1 tags after filtering in treatment: 15578472 INFO @ Sat, 11 Dec 2021 07:08:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:08:49: #1 finished! INFO @ Sat, 11 Dec 2021 07:08:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:08:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:08:50: #2 number of paired peaks: 156 WARNING @ Sat, 11 Dec 2021 07:08:50: Fewer paired peaks (156) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 156 pairs to build model! INFO @ Sat, 11 Dec 2021 07:08:50: start model_add_line... INFO @ Sat, 11 Dec 2021 07:08:50: start X-correlation... INFO @ Sat, 11 Dec 2021 07:08:50: end of X-cor INFO @ Sat, 11 Dec 2021 07:08:50: #2 finished! INFO @ Sat, 11 Dec 2021 07:08:50: #2 predicted fragment length is 48 bps INFO @ Sat, 11 Dec 2021 07:08:50: #2 alternative fragment length(s) may be 48 bps INFO @ Sat, 11 Dec 2021 07:08:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.20_model.r WARNING @ Sat, 11 Dec 2021 07:08:50: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:08:50: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sat, 11 Dec 2021 07:08:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 07:08:50: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:08:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:08:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:08:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:08:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.10_summits.bed INFO @ Sat, 11 Dec 2021 07:08:52: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1457 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:09:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:09:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:09:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:09:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689042/SRX8689042.20_summits.bed INFO @ Sat, 11 Dec 2021 07:09:33: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (1045 records, 4 fields): 3 millis CompletedMACS2peakCalling