Job ID = 14167435 SRX = SRX8688946 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 23309621 spots for SRR12174177/SRR12174177.sra Written 23309621 spots for SRR12174177/SRR12174177.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168069 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:06:48 23309621 reads; of these: 23309621 (100.00%) were unpaired; of these: 3745588 (16.07%) aligned 0 times 14854867 (63.73%) aligned exactly 1 time 4709166 (20.20%) aligned >1 times 83.93% overall alignment rate Time searching: 00:06:49 Overall time: 00:06:49 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] 1970472 / 19564033 = 0.1007 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 12:31:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.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 12:31:20: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:31:20: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:31:25: 1000000 INFO @ Fri, 10 Dec 2021 12:31:30: 2000000 INFO @ Fri, 10 Dec 2021 12:31:34: 3000000 INFO @ Fri, 10 Dec 2021 12:31:39: 4000000 INFO @ Fri, 10 Dec 2021 12:31:44: 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 @ Fri, 10 Dec 2021 12:31:49: 6000000 INFO @ Fri, 10 Dec 2021 12:31:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.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 12:31:50: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:31:50: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:31:54: 7000000 INFO @ Fri, 10 Dec 2021 12:31:55: 1000000 INFO @ Fri, 10 Dec 2021 12:31:59: 8000000 INFO @ Fri, 10 Dec 2021 12:32:00: 2000000 INFO @ Fri, 10 Dec 2021 12:32:05: 9000000 INFO @ Fri, 10 Dec 2021 12:32:05: 3000000 INFO @ Fri, 10 Dec 2021 12:32:10: 10000000 INFO @ Fri, 10 Dec 2021 12:32:11: 4000000 INFO @ Fri, 10 Dec 2021 12:32:15: 11000000 INFO @ Fri, 10 Dec 2021 12:32:16: 5000000 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 12:32:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.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 12:32:20: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:32:20: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:32:20: 12000000 INFO @ Fri, 10 Dec 2021 12:32:21: 6000000 INFO @ Fri, 10 Dec 2021 12:32:25: 1000000 INFO @ Fri, 10 Dec 2021 12:32:25: 13000000 INFO @ Fri, 10 Dec 2021 12:32:26: 7000000 INFO @ Fri, 10 Dec 2021 12:32:30: 2000000 INFO @ Fri, 10 Dec 2021 12:32:31: 14000000 INFO @ Fri, 10 Dec 2021 12:32:32: 8000000 INFO @ Fri, 10 Dec 2021 12:32:36: 3000000 INFO @ Fri, 10 Dec 2021 12:32:36: 15000000 INFO @ Fri, 10 Dec 2021 12:32:37: 9000000 INFO @ Fri, 10 Dec 2021 12:32:41: 4000000 INFO @ Fri, 10 Dec 2021 12:32:41: 16000000 INFO @ Fri, 10 Dec 2021 12:32:42: 10000000 INFO @ Fri, 10 Dec 2021 12:32:46: 5000000 INFO @ Fri, 10 Dec 2021 12:32:46: 17000000 INFO @ Fri, 10 Dec 2021 12:32:47: 11000000 INFO @ Fri, 10 Dec 2021 12:32:49: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:32:49: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:32:49: #1 total tags in treatment: 17593561 INFO @ Fri, 10 Dec 2021 12:32:49: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:32:49: #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 12:32:50: #1 tags after filtering in treatment: 17593561 INFO @ Fri, 10 Dec 2021 12:32:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:32:50: #1 finished! INFO @ Fri, 10 Dec 2021 12:32:50: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:32:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:32:51: #2 number of paired peaks: 119 WARNING @ Fri, 10 Dec 2021 12:32:51: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Fri, 10 Dec 2021 12:32:51: start model_add_line... INFO @ Fri, 10 Dec 2021 12:32:51: start X-correlation... INFO @ Fri, 10 Dec 2021 12:32:51: end of X-cor INFO @ Fri, 10 Dec 2021 12:32:51: #2 finished! INFO @ Fri, 10 Dec 2021 12:32:51: #2 predicted fragment length is 45 bps INFO @ Fri, 10 Dec 2021 12:32:51: #2 alternative fragment length(s) may be 45 bps INFO @ Fri, 10 Dec 2021 12:32:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.05_model.r WARNING @ Fri, 10 Dec 2021 12:32:51: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:32:51: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Fri, 10 Dec 2021 12:32:51: #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 12:32:51: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:32:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:32:51: 6000000 INFO @ Fri, 10 Dec 2021 12:32:53: 12000000 INFO @ Fri, 10 Dec 2021 12:32:56: 7000000 INFO @ Fri, 10 Dec 2021 12:32:58: 13000000 INFO @ Fri, 10 Dec 2021 12:33:02: 8000000 INFO @ Fri, 10 Dec 2021 12:33:03: 14000000 INFO @ Fri, 10 Dec 2021 12:33:07: 9000000 INFO @ Fri, 10 Dec 2021 12:33:08: 15000000 INFO @ Fri, 10 Dec 2021 12:33:12: 10000000 INFO @ Fri, 10 Dec 2021 12:33:13: 16000000 INFO @ Fri, 10 Dec 2021 12:33:17: 11000000 INFO @ Fri, 10 Dec 2021 12:33:19: 17000000 INFO @ Fri, 10 Dec 2021 12:33:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:33:22: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:33:22: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:33:22: #1 total tags in treatment: 17593561 INFO @ Fri, 10 Dec 2021 12:33:22: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:33:22: #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 12:33:22: #1 tags after filtering in treatment: 17593561 INFO @ Fri, 10 Dec 2021 12:33:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:33:22: #1 finished! INFO @ Fri, 10 Dec 2021 12:33:22: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:33:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:33:23: 12000000 INFO @ Fri, 10 Dec 2021 12:33:23: #2 number of paired peaks: 119 WARNING @ Fri, 10 Dec 2021 12:33:23: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Fri, 10 Dec 2021 12:33:23: start model_add_line... INFO @ Fri, 10 Dec 2021 12:33:23: start X-correlation... INFO @ Fri, 10 Dec 2021 12:33:23: end of X-cor INFO @ Fri, 10 Dec 2021 12:33:23: #2 finished! INFO @ Fri, 10 Dec 2021 12:33:23: #2 predicted fragment length is 45 bps INFO @ Fri, 10 Dec 2021 12:33:23: #2 alternative fragment length(s) may be 45 bps INFO @ Fri, 10 Dec 2021 12:33:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.10_model.r WARNING @ Fri, 10 Dec 2021 12:33:23: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:33:23: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Fri, 10 Dec 2021 12:33:23: #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 12:33:23: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:33:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:33:28: 13000000 INFO @ Fri, 10 Dec 2021 12:33:33: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:33:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:33:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:33:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.05_summits.bed INFO @ Fri, 10 Dec 2021 12:33:36: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1758 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:33:38: 15000000 INFO @ Fri, 10 Dec 2021 12:33:43: 16000000 INFO @ Fri, 10 Dec 2021 12:33:48: 17000000 INFO @ Fri, 10 Dec 2021 12:33:51: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:33:51: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:33:51: #1 total tags in treatment: 17593561 INFO @ Fri, 10 Dec 2021 12:33:51: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:33:51: #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 12:33:51: #1 tags after filtering in treatment: 17593561 INFO @ Fri, 10 Dec 2021 12:33:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:33:51: #1 finished! INFO @ Fri, 10 Dec 2021 12:33:51: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:33:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:33:52: #2 number of paired peaks: 119 WARNING @ Fri, 10 Dec 2021 12:33:52: Fewer paired peaks (119) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 119 pairs to build model! INFO @ Fri, 10 Dec 2021 12:33:52: start model_add_line... INFO @ Fri, 10 Dec 2021 12:33:52: start X-correlation... INFO @ Fri, 10 Dec 2021 12:33:52: end of X-cor INFO @ Fri, 10 Dec 2021 12:33:52: #2 finished! INFO @ Fri, 10 Dec 2021 12:33:52: #2 predicted fragment length is 45 bps INFO @ Fri, 10 Dec 2021 12:33:52: #2 alternative fragment length(s) may be 45 bps INFO @ Fri, 10 Dec 2021 12:33:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.20_model.r WARNING @ Fri, 10 Dec 2021 12:33:52: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:33:52: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Fri, 10 Dec 2021 12:33:52: #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 12:33:52: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:33:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:33:53: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:34:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:34:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:34:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.10_summits.bed INFO @ Fri, 10 Dec 2021 12:34:08: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (1367 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:34:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:34:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:34:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:34:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688946/SRX8688946.20_summits.bed INFO @ Fri, 10 Dec 2021 12:34:36: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1044 records, 4 fields): 2 millis CompletedMACS2peakCalling