Job ID = 14167482 SRX = SRX8688953 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7435205 spots for SRR12174224/SRR12174224.sra Written 7435205 spots for SRR12174224/SRR12174224.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168073 ("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: 00:02:07 7435205 reads; of these: 7435205 (100.00%) were unpaired; of these: 645053 (8.68%) aligned 0 times 5437985 (73.14%) aligned exactly 1 time 1352167 (18.19%) aligned >1 times 91.32% overall alignment rate Time searching: 00:02:07 Overall time: 00:02:07 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_rmdupse_core] 332716 / 6790152 = 0.0490 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 12:29:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.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 12:29:47: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:29:47: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:29:52: 1000000 INFO @ Fri, 10 Dec 2021 12:29:58: 2000000 INFO @ Fri, 10 Dec 2021 12:30:04: 3000000 INFO @ Fri, 10 Dec 2021 12:30:10: 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 @ Fri, 10 Dec 2021 12:30:16: 5000000 INFO @ Fri, 10 Dec 2021 12:30:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.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 12:30:17: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:30:17: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:30:22: 1000000 INFO @ Fri, 10 Dec 2021 12:30:23: 6000000 INFO @ Fri, 10 Dec 2021 12:30:26: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:30:26: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:30:26: #1 total tags in treatment: 6457436 INFO @ Fri, 10 Dec 2021 12:30:26: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:30:26: #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 12:30:26: #1 tags after filtering in treatment: 6457436 INFO @ Fri, 10 Dec 2021 12:30:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:30:26: #1 finished! INFO @ Fri, 10 Dec 2021 12:30:26: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:30:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:30:26: #2 number of paired peaks: 115 WARNING @ Fri, 10 Dec 2021 12:30:26: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Fri, 10 Dec 2021 12:30:26: start model_add_line... INFO @ Fri, 10 Dec 2021 12:30:26: start X-correlation... INFO @ Fri, 10 Dec 2021 12:30:26: end of X-cor INFO @ Fri, 10 Dec 2021 12:30:26: #2 finished! INFO @ Fri, 10 Dec 2021 12:30:26: #2 predicted fragment length is 52 bps INFO @ Fri, 10 Dec 2021 12:30:26: #2 alternative fragment length(s) may be 52 bps INFO @ Fri, 10 Dec 2021 12:30:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.05_model.r WARNING @ Fri, 10 Dec 2021 12:30:26: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:30:26: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Fri, 10 Dec 2021 12:30:26: #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 12:30:26: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:30:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:30:28: 2000000 INFO @ Fri, 10 Dec 2021 12:30:33: 3000000 INFO @ Fri, 10 Dec 2021 12:30:38: 4000000 INFO @ Fri, 10 Dec 2021 12:30:39: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:30:43: 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 12:30:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:30:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:30:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.05_summits.bed INFO @ Fri, 10 Dec 2021 12:30:46: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1090 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:30:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.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 12:30:47: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:30:47: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:30:48: 6000000 INFO @ Fri, 10 Dec 2021 12:30:50: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:30:50: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:30:50: #1 total tags in treatment: 6457436 INFO @ Fri, 10 Dec 2021 12:30:50: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:30:50: #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 12:30:50: #1 tags after filtering in treatment: 6457436 INFO @ Fri, 10 Dec 2021 12:30:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:30:50: #1 finished! INFO @ Fri, 10 Dec 2021 12:30:50: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:30:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:30:51: #2 number of paired peaks: 115 WARNING @ Fri, 10 Dec 2021 12:30:51: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Fri, 10 Dec 2021 12:30:51: start model_add_line... INFO @ Fri, 10 Dec 2021 12:30:51: start X-correlation... INFO @ Fri, 10 Dec 2021 12:30:51: end of X-cor INFO @ Fri, 10 Dec 2021 12:30:51: #2 finished! INFO @ Fri, 10 Dec 2021 12:30:51: #2 predicted fragment length is 52 bps INFO @ Fri, 10 Dec 2021 12:30:51: #2 alternative fragment length(s) may be 52 bps INFO @ Fri, 10 Dec 2021 12:30:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.10_model.r WARNING @ Fri, 10 Dec 2021 12:30:51: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:30:51: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Fri, 10 Dec 2021 12:30:51: #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 12:30:51: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:30:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:30:52: 1000000 INFO @ Fri, 10 Dec 2021 12:30:57: 2000000 INFO @ Fri, 10 Dec 2021 12:31:02: 3000000 INFO @ Fri, 10 Dec 2021 12:31:03: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:31:07: 4000000 INFO @ Fri, 10 Dec 2021 12:31:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:31:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:31:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.10_summits.bed INFO @ Fri, 10 Dec 2021 12:31:10: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (853 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:31:11: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:31:16: 6000000 INFO @ Fri, 10 Dec 2021 12:31:19: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:31:19: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:31:19: #1 total tags in treatment: 6457436 INFO @ Fri, 10 Dec 2021 12:31:19: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:31:19: #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 12:31:19: #1 tags after filtering in treatment: 6457436 INFO @ Fri, 10 Dec 2021 12:31:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:31:19: #1 finished! INFO @ Fri, 10 Dec 2021 12:31:19: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:31:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:31:19: #2 number of paired peaks: 115 WARNING @ Fri, 10 Dec 2021 12:31:19: Fewer paired peaks (115) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 115 pairs to build model! INFO @ Fri, 10 Dec 2021 12:31:19: start model_add_line... INFO @ Fri, 10 Dec 2021 12:31:19: start X-correlation... INFO @ Fri, 10 Dec 2021 12:31:19: end of X-cor INFO @ Fri, 10 Dec 2021 12:31:19: #2 finished! INFO @ Fri, 10 Dec 2021 12:31:19: #2 predicted fragment length is 52 bps INFO @ Fri, 10 Dec 2021 12:31:19: #2 alternative fragment length(s) may be 52 bps INFO @ Fri, 10 Dec 2021 12:31:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.20_model.r WARNING @ Fri, 10 Dec 2021 12:31:19: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:31:19: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Fri, 10 Dec 2021 12:31:19: #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 12:31:19: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:31:19: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:31:32: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:31:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:31:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:31:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688953/SRX8688953.20_summits.bed INFO @ Fri, 10 Dec 2021 12:31:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (524 records, 4 fields): 13 millis CompletedMACS2peakCalling