Job ID = 14170582 SRX = SRX9720899 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 22693016 spots for SRR13291889/SRR13291889.sra Written 22693016 spots for SRR13291889/SRR13291889.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171003 ("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: 00:08:11 22693016 reads; of these: 22693016 (100.00%) were unpaired; of these: 740120 (3.26%) aligned 0 times 14625587 (64.45%) aligned exactly 1 time 7327309 (32.29%) aligned >1 times 96.74% overall alignment rate Time searching: 00:08:11 Overall time: 00:08:11 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] 3774770 / 21952896 = 0.1719 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 07:33:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.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 07:33:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:33:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:33:49: 1000000 INFO @ Sat, 11 Dec 2021 07:33:54: 2000000 INFO @ Sat, 11 Dec 2021 07:33:58: 3000000 INFO @ Sat, 11 Dec 2021 07:34:03: 4000000 INFO @ Sat, 11 Dec 2021 07:34:08: 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 07:34:12: 6000000 INFO @ Sat, 11 Dec 2021 07:34:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.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 07:34:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:34:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:34:17: 7000000 INFO @ Sat, 11 Dec 2021 07:34:19: 1000000 INFO @ Sat, 11 Dec 2021 07:34:22: 8000000 INFO @ Sat, 11 Dec 2021 07:34:24: 2000000 INFO @ Sat, 11 Dec 2021 07:34:27: 9000000 INFO @ Sat, 11 Dec 2021 07:34:29: 3000000 INFO @ Sat, 11 Dec 2021 07:34:32: 10000000 INFO @ Sat, 11 Dec 2021 07:34:34: 4000000 INFO @ Sat, 11 Dec 2021 07:34:37: 11000000 INFO @ Sat, 11 Dec 2021 07:34:39: 5000000 INFO @ Sat, 11 Dec 2021 07:34:42: 12000000 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 07:34:44: 6000000 INFO @ Sat, 11 Dec 2021 07:34:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.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 07:34:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:34:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:34:47: 13000000 INFO @ Sat, 11 Dec 2021 07:34:49: 7000000 INFO @ Sat, 11 Dec 2021 07:34:49: 1000000 INFO @ Sat, 11 Dec 2021 07:34:52: 14000000 INFO @ Sat, 11 Dec 2021 07:34:53: 8000000 INFO @ Sat, 11 Dec 2021 07:34:54: 2000000 INFO @ Sat, 11 Dec 2021 07:34:57: 15000000 INFO @ Sat, 11 Dec 2021 07:34:58: 9000000 INFO @ Sat, 11 Dec 2021 07:34:59: 3000000 INFO @ Sat, 11 Dec 2021 07:35:01: 16000000 INFO @ Sat, 11 Dec 2021 07:35:03: 10000000 INFO @ Sat, 11 Dec 2021 07:35:04: 4000000 INFO @ Sat, 11 Dec 2021 07:35:06: 17000000 INFO @ Sat, 11 Dec 2021 07:35:08: 11000000 INFO @ Sat, 11 Dec 2021 07:35:09: 5000000 INFO @ Sat, 11 Dec 2021 07:35:11: 18000000 INFO @ Sat, 11 Dec 2021 07:35:13: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:35:13: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:35:13: #1 total tags in treatment: 18178126 INFO @ Sat, 11 Dec 2021 07:35:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:35:13: #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 07:35:13: #1 tags after filtering in treatment: 18178126 INFO @ Sat, 11 Dec 2021 07:35:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:35:13: #1 finished! INFO @ Sat, 11 Dec 2021 07:35:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:35:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:35:13: 12000000 INFO @ Sat, 11 Dec 2021 07:35:14: 6000000 INFO @ Sat, 11 Dec 2021 07:35:14: #2 number of paired peaks: 528 WARNING @ Sat, 11 Dec 2021 07:35:14: Fewer paired peaks (528) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 528 pairs to build model! INFO @ Sat, 11 Dec 2021 07:35:14: start model_add_line... INFO @ Sat, 11 Dec 2021 07:35:14: start X-correlation... INFO @ Sat, 11 Dec 2021 07:35:14: end of X-cor INFO @ Sat, 11 Dec 2021 07:35:14: #2 finished! INFO @ Sat, 11 Dec 2021 07:35:14: #2 predicted fragment length is 44 bps INFO @ Sat, 11 Dec 2021 07:35:14: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sat, 11 Dec 2021 07:35:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.05_model.r WARNING @ Sat, 11 Dec 2021 07:35:14: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:35:14: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sat, 11 Dec 2021 07:35:14: #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 07:35:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:35:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:35:18: 13000000 INFO @ Sat, 11 Dec 2021 07:35:19: 7000000 INFO @ Sat, 11 Dec 2021 07:35:23: 14000000 INFO @ Sat, 11 Dec 2021 07:35:24: 8000000 INFO @ Sat, 11 Dec 2021 07:35:28: 15000000 INFO @ Sat, 11 Dec 2021 07:35:28: 9000000 INFO @ Sat, 11 Dec 2021 07:35:33: 16000000 INFO @ Sat, 11 Dec 2021 07:35:33: 10000000 INFO @ Sat, 11 Dec 2021 07:35:38: 17000000 INFO @ Sat, 11 Dec 2021 07:35:38: 11000000 INFO @ Sat, 11 Dec 2021 07:35:43: 18000000 INFO @ Sat, 11 Dec 2021 07:35:43: 12000000 INFO @ Sat, 11 Dec 2021 07:35:44: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:35:44: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:35:44: #1 total tags in treatment: 18178126 INFO @ Sat, 11 Dec 2021 07:35:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:35:44: #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 07:35:44: #1 tags after filtering in treatment: 18178126 INFO @ Sat, 11 Dec 2021 07:35:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:35:44: #1 finished! INFO @ Sat, 11 Dec 2021 07:35:44: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:35:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:35:45: #2 number of paired peaks: 528 WARNING @ Sat, 11 Dec 2021 07:35:45: Fewer paired peaks (528) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 528 pairs to build model! INFO @ Sat, 11 Dec 2021 07:35:45: start model_add_line... INFO @ Sat, 11 Dec 2021 07:35:45: start X-correlation... INFO @ Sat, 11 Dec 2021 07:35:46: end of X-cor INFO @ Sat, 11 Dec 2021 07:35:46: #2 finished! INFO @ Sat, 11 Dec 2021 07:35:46: #2 predicted fragment length is 44 bps INFO @ Sat, 11 Dec 2021 07:35:46: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sat, 11 Dec 2021 07:35:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.10_model.r WARNING @ Sat, 11 Dec 2021 07:35:46: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:35:46: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sat, 11 Dec 2021 07:35:46: #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 07:35:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:35:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:35:48: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:35:48: 13000000 INFO @ Sat, 11 Dec 2021 07:35:53: 14000000 INFO @ Sat, 11 Dec 2021 07:35:57: 15000000 INFO @ Sat, 11 Dec 2021 07:36:02: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:36:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:36:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:36:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.05_summits.bed INFO @ Sat, 11 Dec 2021 07:36:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3408 records, 4 fields): 53 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:36:07: 17000000 INFO @ Sat, 11 Dec 2021 07:36:12: 18000000 INFO @ Sat, 11 Dec 2021 07:36:13: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:36:13: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:36:13: #1 total tags in treatment: 18178126 INFO @ Sat, 11 Dec 2021 07:36:13: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:36:13: #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 07:36:13: #1 tags after filtering in treatment: 18178126 INFO @ Sat, 11 Dec 2021 07:36:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:36:13: #1 finished! INFO @ Sat, 11 Dec 2021 07:36:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:36:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:36:14: #2 number of paired peaks: 528 WARNING @ Sat, 11 Dec 2021 07:36:14: Fewer paired peaks (528) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 528 pairs to build model! INFO @ Sat, 11 Dec 2021 07:36:14: start model_add_line... INFO @ Sat, 11 Dec 2021 07:36:14: start X-correlation... INFO @ Sat, 11 Dec 2021 07:36:14: end of X-cor INFO @ Sat, 11 Dec 2021 07:36:14: #2 finished! INFO @ Sat, 11 Dec 2021 07:36:14: #2 predicted fragment length is 44 bps INFO @ Sat, 11 Dec 2021 07:36:14: #2 alternative fragment length(s) may be 4,44 bps INFO @ Sat, 11 Dec 2021 07:36:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.20_model.r WARNING @ Sat, 11 Dec 2021 07:36:14: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:36:14: #2 You may need to consider one of the other alternative d(s): 4,44 WARNING @ Sat, 11 Dec 2021 07:36:14: #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 07:36:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:36:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:36:19: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:36:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:36:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:36:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.10_summits.bed INFO @ Sat, 11 Dec 2021 07:36:36: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2290 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:36:47: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:37:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:37:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:37:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX9720899/SRX9720899.20_summits.bed INFO @ Sat, 11 Dec 2021 07:37:03: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1214 records, 4 fields): 2 millis CompletedMACS2peakCalling