Job ID = 14168082 SRX = SRX8688976 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14476032 spots for SRR12174345/SRR12174345.sra Written 14476032 spots for SRR12174345/SRR12174345.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168844 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:57 14476032 reads; of these: 14476032 (100.00%) were unpaired; of these: 292056 (2.02%) aligned 0 times 9968816 (68.86%) aligned exactly 1 time 4215160 (29.12%) aligned >1 times 97.98% overall alignment rate Time searching: 00:05:58 Overall time: 00:05:58 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] 1150490 / 14183976 = 0.0811 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 @ Fri, 10 Dec 2021 15:21:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.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 @ Fri, 10 Dec 2021 15:21:35: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:21:35: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:21:42: 1000000 INFO @ Fri, 10 Dec 2021 15:21:49: 2000000 INFO @ Fri, 10 Dec 2021 15:21:56: 3000000 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 @ Fri, 10 Dec 2021 15:22:03: 4000000 INFO @ Fri, 10 Dec 2021 15:22:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.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 @ Fri, 10 Dec 2021 15:22:04: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:22:04: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:22:11: 5000000 INFO @ Fri, 10 Dec 2021 15:22:12: 1000000 INFO @ Fri, 10 Dec 2021 15:22:19: 2000000 INFO @ Fri, 10 Dec 2021 15:22:19: 6000000 INFO @ Fri, 10 Dec 2021 15:22:27: 3000000 INFO @ Fri, 10 Dec 2021 15:22:27: 7000000 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 @ Fri, 10 Dec 2021 15:22:34: 4000000 INFO @ Fri, 10 Dec 2021 15:22:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.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 @ Fri, 10 Dec 2021 15:22:35: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:22:35: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:22:35: 8000000 INFO @ Fri, 10 Dec 2021 15:22:42: 5000000 INFO @ Fri, 10 Dec 2021 15:22:43: 1000000 INFO @ Fri, 10 Dec 2021 15:22:43: 9000000 INFO @ Fri, 10 Dec 2021 15:22:50: 6000000 INFO @ Fri, 10 Dec 2021 15:22:51: 2000000 INFO @ Fri, 10 Dec 2021 15:22:51: 10000000 INFO @ Fri, 10 Dec 2021 15:22:59: 7000000 INFO @ Fri, 10 Dec 2021 15:22:59: 3000000 INFO @ Fri, 10 Dec 2021 15:23:00: 11000000 INFO @ Fri, 10 Dec 2021 15:23:06: 8000000 INFO @ Fri, 10 Dec 2021 15:23:08: 4000000 INFO @ Fri, 10 Dec 2021 15:23:09: 12000000 INFO @ Fri, 10 Dec 2021 15:23:15: 9000000 INFO @ Fri, 10 Dec 2021 15:23:16: 5000000 INFO @ Fri, 10 Dec 2021 15:23:17: 13000000 INFO @ Fri, 10 Dec 2021 15:23:17: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:23:17: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:23:17: #1 total tags in treatment: 13033486 INFO @ Fri, 10 Dec 2021 15:23:17: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:23:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:23:17: #1 tags after filtering in treatment: 13033486 INFO @ Fri, 10 Dec 2021 15:23:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:23:17: #1 finished! INFO @ Fri, 10 Dec 2021 15:23:17: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:23:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:23:18: #2 number of paired peaks: 202 WARNING @ Fri, 10 Dec 2021 15:23:18: 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 @ Fri, 10 Dec 2021 15:23:18: start model_add_line... INFO @ Fri, 10 Dec 2021 15:23:18: start X-correlation... INFO @ Fri, 10 Dec 2021 15:23:18: end of X-cor INFO @ Fri, 10 Dec 2021 15:23:18: #2 finished! INFO @ Fri, 10 Dec 2021 15:23:18: #2 predicted fragment length is 48 bps INFO @ Fri, 10 Dec 2021 15:23:18: #2 alternative fragment length(s) may be 48 bps INFO @ Fri, 10 Dec 2021 15:23:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.05_model.r WARNING @ Fri, 10 Dec 2021 15:23:18: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:23:18: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Fri, 10 Dec 2021 15:23:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 15:23:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:23:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:23:23: 10000000 INFO @ Fri, 10 Dec 2021 15:23:24: 6000000 INFO @ Fri, 10 Dec 2021 15:23:31: 11000000 INFO @ Fri, 10 Dec 2021 15:23:32: 7000000 INFO @ Fri, 10 Dec 2021 15:23:39: 12000000 INFO @ Fri, 10 Dec 2021 15:23:39: 8000000 INFO @ Fri, 10 Dec 2021 15:23:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:23:47: 9000000 INFO @ Fri, 10 Dec 2021 15:23:47: 13000000 INFO @ Fri, 10 Dec 2021 15:23:47: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:23:47: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:23:47: #1 total tags in treatment: 13033486 INFO @ Fri, 10 Dec 2021 15:23:47: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:23:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:23:48: #1 tags after filtering in treatment: 13033486 INFO @ Fri, 10 Dec 2021 15:23:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:23:48: #1 finished! INFO @ Fri, 10 Dec 2021 15:23:48: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:23:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:23:49: #2 number of paired peaks: 202 WARNING @ Fri, 10 Dec 2021 15:23:49: 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 @ Fri, 10 Dec 2021 15:23:49: start model_add_line... INFO @ Fri, 10 Dec 2021 15:23:49: start X-correlation... INFO @ Fri, 10 Dec 2021 15:23:49: end of X-cor INFO @ Fri, 10 Dec 2021 15:23:49: #2 finished! INFO @ Fri, 10 Dec 2021 15:23:49: #2 predicted fragment length is 48 bps INFO @ Fri, 10 Dec 2021 15:23:49: #2 alternative fragment length(s) may be 48 bps INFO @ Fri, 10 Dec 2021 15:23:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.10_model.r WARNING @ Fri, 10 Dec 2021 15:23:49: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:23:49: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Fri, 10 Dec 2021 15:23:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 15:23:49: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:23:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:23:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.05_peaks.xls INFO @ Fri, 10 Dec 2021 15:23:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:23:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.05_summits.bed INFO @ Fri, 10 Dec 2021 15:23:54: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2675 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:23:55: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 15:24:02: 11000000 INFO @ Fri, 10 Dec 2021 15:24:09: 12000000 INFO @ Fri, 10 Dec 2021 15:24:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:24:16: 13000000 INFO @ Fri, 10 Dec 2021 15:24:17: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:24:17: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:24:17: #1 total tags in treatment: 13033486 INFO @ Fri, 10 Dec 2021 15:24:17: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:24:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 15:24:17: #1 tags after filtering in treatment: 13033486 INFO @ Fri, 10 Dec 2021 15:24:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:24:17: #1 finished! INFO @ Fri, 10 Dec 2021 15:24:17: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:24:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:24:18: #2 number of paired peaks: 202 WARNING @ Fri, 10 Dec 2021 15:24:18: 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 @ Fri, 10 Dec 2021 15:24:18: start model_add_line... INFO @ Fri, 10 Dec 2021 15:24:18: start X-correlation... INFO @ Fri, 10 Dec 2021 15:24:18: end of X-cor INFO @ Fri, 10 Dec 2021 15:24:18: #2 finished! INFO @ Fri, 10 Dec 2021 15:24:18: #2 predicted fragment length is 48 bps INFO @ Fri, 10 Dec 2021 15:24:18: #2 alternative fragment length(s) may be 48 bps INFO @ Fri, 10 Dec 2021 15:24:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.20_model.r WARNING @ Fri, 10 Dec 2021 15:24:18: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:24:18: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Fri, 10 Dec 2021 15:24:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 15:24:18: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:24:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:24:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.10_peaks.xls INFO @ Fri, 10 Dec 2021 15:24:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:24:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.10_summits.bed INFO @ Fri, 10 Dec 2021 15:24:24: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1382 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 15:24:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:24:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.20_peaks.xls INFO @ Fri, 10 Dec 2021 15:24:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:24:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688976/SRX8688976.20_summits.bed INFO @ Fri, 10 Dec 2021 15:24:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (903 records, 4 fields): 3 millis CompletedMACS2peakCalling