Job ID = 14170382 SRX = SRX8689006 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 18158016 spots for SRR12174295/SRR12174295.sra Written 18158016 spots for SRR12174295/SRR12174295.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170781 ("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: 00:06:14 18158016 reads; of these: 18158016 (100.00%) were unpaired; of these: 514852 (2.84%) aligned 0 times 12511631 (68.90%) aligned exactly 1 time 5131533 (28.26%) aligned >1 times 97.16% overall alignment rate Time searching: 00:06:14 Overall time: 00:06:14 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] 1605246 / 17643164 = 0.0910 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 06:40:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.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 06:40:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:40:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:40:08: 1000000 INFO @ Sat, 11 Dec 2021 06:40:13: 2000000 INFO @ Sat, 11 Dec 2021 06:40:17: 3000000 INFO @ Sat, 11 Dec 2021 06:40:22: 4000000 INFO @ Sat, 11 Dec 2021 06:40:27: 5000000 INFO @ Sat, 11 Dec 2021 06:40:31: 6000000 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 06:40:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.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 06:40:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:40:34: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:40:36: 7000000 INFO @ Sat, 11 Dec 2021 06:40:38: 1000000 INFO @ Sat, 11 Dec 2021 06:40:41: 8000000 INFO @ Sat, 11 Dec 2021 06:40:43: 2000000 INFO @ Sat, 11 Dec 2021 06:40:46: 9000000 INFO @ Sat, 11 Dec 2021 06:40:48: 3000000 INFO @ Sat, 11 Dec 2021 06:40:50: 10000000 INFO @ Sat, 11 Dec 2021 06:40:52: 4000000 INFO @ Sat, 11 Dec 2021 06:40:55: 11000000 INFO @ Sat, 11 Dec 2021 06:40:57: 5000000 INFO @ Sat, 11 Dec 2021 06:41:00: 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 06:41:02: 6000000 INFO @ Sat, 11 Dec 2021 06:41:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.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 06:41:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:41:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:41:04: 13000000 INFO @ Sat, 11 Dec 2021 06:41:07: 7000000 INFO @ Sat, 11 Dec 2021 06:41:09: 1000000 INFO @ Sat, 11 Dec 2021 06:41:09: 14000000 INFO @ Sat, 11 Dec 2021 06:41:11: 8000000 INFO @ Sat, 11 Dec 2021 06:41:14: 2000000 INFO @ Sat, 11 Dec 2021 06:41:14: 15000000 INFO @ Sat, 11 Dec 2021 06:41:16: 9000000 INFO @ Sat, 11 Dec 2021 06:41:19: 3000000 INFO @ Sat, 11 Dec 2021 06:41:19: 16000000 INFO @ Sat, 11 Dec 2021 06:41:19: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:41:19: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:41:19: #1 total tags in treatment: 16037918 INFO @ Sat, 11 Dec 2021 06:41:19: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:41:19: #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 06:41:19: #1 tags after filtering in treatment: 16037918 INFO @ Sat, 11 Dec 2021 06:41:19: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:41:19: #1 finished! INFO @ Sat, 11 Dec 2021 06:41:19: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:41:19: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:41:20: #2 number of paired peaks: 144 WARNING @ Sat, 11 Dec 2021 06:41:20: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Sat, 11 Dec 2021 06:41:20: start model_add_line... INFO @ Sat, 11 Dec 2021 06:41:20: start X-correlation... INFO @ Sat, 11 Dec 2021 06:41:20: end of X-cor INFO @ Sat, 11 Dec 2021 06:41:20: #2 finished! INFO @ Sat, 11 Dec 2021 06:41:20: #2 predicted fragment length is 43 bps INFO @ Sat, 11 Dec 2021 06:41:20: #2 alternative fragment length(s) may be 43 bps INFO @ Sat, 11 Dec 2021 06:41:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.05_model.r WARNING @ Sat, 11 Dec 2021 06:41:20: #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, 11 Dec 2021 06:41:20: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Sat, 11 Dec 2021 06:41:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 06:41:20: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:41:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:41:21: 10000000 INFO @ Sat, 11 Dec 2021 06:41:23: 4000000 INFO @ Sat, 11 Dec 2021 06:41:26: 11000000 INFO @ Sat, 11 Dec 2021 06:41:28: 5000000 INFO @ Sat, 11 Dec 2021 06:41:30: 12000000 INFO @ Sat, 11 Dec 2021 06:41:33: 6000000 INFO @ Sat, 11 Dec 2021 06:41:35: 13000000 INFO @ Sat, 11 Dec 2021 06:41:38: 7000000 INFO @ Sat, 11 Dec 2021 06:41:40: 14000000 INFO @ Sat, 11 Dec 2021 06:41:42: 8000000 INFO @ Sat, 11 Dec 2021 06:41:45: 15000000 INFO @ Sat, 11 Dec 2021 06:41:47: 9000000 INFO @ Sat, 11 Dec 2021 06:41:48: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:41:49: 16000000 INFO @ Sat, 11 Dec 2021 06:41:49: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:41:49: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:41:49: #1 total tags in treatment: 16037918 INFO @ Sat, 11 Dec 2021 06:41:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:41:49: #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 06:41:50: #1 tags after filtering in treatment: 16037918 INFO @ Sat, 11 Dec 2021 06:41:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:41:50: #1 finished! INFO @ Sat, 11 Dec 2021 06:41:50: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:41:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:41:51: #2 number of paired peaks: 144 WARNING @ Sat, 11 Dec 2021 06:41:51: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Sat, 11 Dec 2021 06:41:51: start model_add_line... INFO @ Sat, 11 Dec 2021 06:41:51: start X-correlation... INFO @ Sat, 11 Dec 2021 06:41:51: end of X-cor INFO @ Sat, 11 Dec 2021 06:41:51: #2 finished! INFO @ Sat, 11 Dec 2021 06:41:51: #2 predicted fragment length is 43 bps INFO @ Sat, 11 Dec 2021 06:41:51: #2 alternative fragment length(s) may be 43 bps INFO @ Sat, 11 Dec 2021 06:41:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.10_model.r WARNING @ Sat, 11 Dec 2021 06:41:51: #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, 11 Dec 2021 06:41:51: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Sat, 11 Dec 2021 06:41:51: #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 06:41:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:41:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:41:52: 10000000 INFO @ Sat, 11 Dec 2021 06:41:57: 11000000 INFO @ Sat, 11 Dec 2021 06:42:01: 12000000 INFO @ Sat, 11 Dec 2021 06:42:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:42:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:42:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.05_summits.bed INFO @ Sat, 11 Dec 2021 06:42:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2184 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:42:06: 13000000 INFO @ Sat, 11 Dec 2021 06:42:10: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:42:15: 15000000 INFO @ Sat, 11 Dec 2021 06:42:18: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:42:20: 16000000 INFO @ Sat, 11 Dec 2021 06:42:20: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:42:20: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:42:20: #1 total tags in treatment: 16037918 INFO @ Sat, 11 Dec 2021 06:42:20: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:42:20: #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 06:42:20: #1 tags after filtering in treatment: 16037918 INFO @ Sat, 11 Dec 2021 06:42:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:42:20: #1 finished! INFO @ Sat, 11 Dec 2021 06:42:20: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:42:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:42:21: #2 number of paired peaks: 144 WARNING @ Sat, 11 Dec 2021 06:42:21: Fewer paired peaks (144) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 144 pairs to build model! INFO @ Sat, 11 Dec 2021 06:42:21: start model_add_line... INFO @ Sat, 11 Dec 2021 06:42:21: start X-correlation... INFO @ Sat, 11 Dec 2021 06:42:21: end of X-cor INFO @ Sat, 11 Dec 2021 06:42:21: #2 finished! INFO @ Sat, 11 Dec 2021 06:42:21: #2 predicted fragment length is 43 bps INFO @ Sat, 11 Dec 2021 06:42:21: #2 alternative fragment length(s) may be 43 bps INFO @ Sat, 11 Dec 2021 06:42:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.20_model.r WARNING @ Sat, 11 Dec 2021 06:42:21: #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, 11 Dec 2021 06:42:21: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Sat, 11 Dec 2021 06:42:21: #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 06:42:21: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:42:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:42:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:42:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:42:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.10_summits.bed INFO @ Sat, 11 Dec 2021 06:42:32: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1296 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:42:49: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:43:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:43:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:43:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689006/SRX8689006.20_summits.bed INFO @ Sat, 11 Dec 2021 06:43:03: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (898 records, 4 fields): 3 millis CompletedMACS2peakCalling