Job ID = 14167248 SRX = SRX8688913 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 5722931 spots for SRR12174314/SRR12174314.sra Written 5722931 spots for SRR12174314/SRR12174314.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167816 ("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: 00:01:52 5722931 reads; of these: 5722931 (100.00%) were unpaired; of these: 222513 (3.89%) aligned 0 times 4094474 (71.55%) aligned exactly 1 time 1405944 (24.57%) aligned >1 times 96.11% overall alignment rate Time searching: 00:01:52 Overall time: 00:01:52 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] 215797 / 5500418 = 0.0392 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 11:20:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.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 11:20:43: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:20:43: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:20:50: 1000000 INFO @ Fri, 10 Dec 2021 11:20:56: 2000000 INFO @ Fri, 10 Dec 2021 11:21:02: 3000000 INFO @ Fri, 10 Dec 2021 11:21:08: 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 11:21:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.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 11:21:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:21:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:21:14: 5000000 INFO @ Fri, 10 Dec 2021 11:21:15: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:21:15: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:21:15: #1 total tags in treatment: 5284621 INFO @ Fri, 10 Dec 2021 11:21:15: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:21:15: #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 11:21:15: #1 tags after filtering in treatment: 5284621 INFO @ Fri, 10 Dec 2021 11:21:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:21:15: #1 finished! INFO @ Fri, 10 Dec 2021 11:21:15: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:21:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:21:16: #2 number of paired peaks: 187 WARNING @ Fri, 10 Dec 2021 11:21:16: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Fri, 10 Dec 2021 11:21:16: start model_add_line... INFO @ Fri, 10 Dec 2021 11:21:16: start X-correlation... INFO @ Fri, 10 Dec 2021 11:21:16: end of X-cor INFO @ Fri, 10 Dec 2021 11:21:16: #2 finished! INFO @ Fri, 10 Dec 2021 11:21:16: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Dec 2021 11:21:16: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 10 Dec 2021 11:21:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.05_model.r WARNING @ Fri, 10 Dec 2021 11:21:16: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:21:16: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 10 Dec 2021 11:21:16: #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 11:21:16: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:21:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:21:19: 1000000 INFO @ Fri, 10 Dec 2021 11:21:24: 2000000 INFO @ Fri, 10 Dec 2021 11:21:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:21:30: 3000000 INFO @ Fri, 10 Dec 2021 11:21:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:21:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:21:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.05_summits.bed INFO @ Fri, 10 Dec 2021 11:21:32: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1006 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:21:35: 4000000 INFO @ Fri, 10 Dec 2021 11:21:40: 5000000 INFO @ Fri, 10 Dec 2021 11:21:41: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:21:41: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:21:41: #1 total tags in treatment: 5284621 INFO @ Fri, 10 Dec 2021 11:21:41: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:21:41: #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 11:21:41: #1 tags after filtering in treatment: 5284621 INFO @ Fri, 10 Dec 2021 11:21:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:21:41: #1 finished! INFO @ Fri, 10 Dec 2021 11:21:41: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:21:41: #2 looking for paired plus/minus strand peaks... 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 11:21:42: #2 number of paired peaks: 187 WARNING @ Fri, 10 Dec 2021 11:21:42: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Fri, 10 Dec 2021 11:21:42: start model_add_line... INFO @ Fri, 10 Dec 2021 11:21:42: start X-correlation... INFO @ Fri, 10 Dec 2021 11:21:42: end of X-cor INFO @ Fri, 10 Dec 2021 11:21:42: #2 finished! INFO @ Fri, 10 Dec 2021 11:21:42: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Dec 2021 11:21:42: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 10 Dec 2021 11:21:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.10_model.r WARNING @ Fri, 10 Dec 2021 11:21:42: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:21:42: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 10 Dec 2021 11:21:42: #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 11:21:42: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:21:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:21:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.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 11:21:43: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:21:43: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:21:50: 1000000 INFO @ Fri, 10 Dec 2021 11:21:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:21:56: 2000000 INFO @ Fri, 10 Dec 2021 11:21:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:21:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:21:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.10_summits.bed INFO @ Fri, 10 Dec 2021 11:21:58: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (790 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:22:02: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:22:08: 4000000 INFO @ Fri, 10 Dec 2021 11:22:14: 5000000 INFO @ Fri, 10 Dec 2021 11:22:15: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:22:15: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:22:15: #1 total tags in treatment: 5284621 INFO @ Fri, 10 Dec 2021 11:22:15: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:22:15: #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 11:22:15: #1 tags after filtering in treatment: 5284621 INFO @ Fri, 10 Dec 2021 11:22:15: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:22:15: #1 finished! INFO @ Fri, 10 Dec 2021 11:22:15: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:22:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:22:16: #2 number of paired peaks: 187 WARNING @ Fri, 10 Dec 2021 11:22:16: Fewer paired peaks (187) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 187 pairs to build model! INFO @ Fri, 10 Dec 2021 11:22:16: start model_add_line... INFO @ Fri, 10 Dec 2021 11:22:16: start X-correlation... INFO @ Fri, 10 Dec 2021 11:22:16: end of X-cor INFO @ Fri, 10 Dec 2021 11:22:16: #2 finished! INFO @ Fri, 10 Dec 2021 11:22:16: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Dec 2021 11:22:16: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 10 Dec 2021 11:22:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.20_model.r WARNING @ Fri, 10 Dec 2021 11:22:16: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:22:16: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 10 Dec 2021 11:22:16: #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 11:22:16: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:22:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:22:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:22:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:22:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:22:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688913/SRX8688913.20_summits.bed INFO @ Fri, 10 Dec 2021 11:22:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (487 records, 4 fields): 1 millis CompletedMACS2peakCalling