Job ID = 14167245 SRX = SRX8688910 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7041888 spots for SRR12174311/SRR12174311.sra Written 7041888 spots for SRR12174311/SRR12174311.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167815 ("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: 00:02:25 7041888 reads; of these: 7041888 (100.00%) were unpaired; of these: 468389 (6.65%) aligned 0 times 4516852 (64.14%) aligned exactly 1 time 2056647 (29.21%) aligned >1 times 93.35% overall alignment rate Time searching: 00:02:25 Overall time: 00:02:25 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] 354831 / 6573499 = 0.0540 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 11:20:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.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 11:20:52: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:20:52: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:20:58: 1000000 INFO @ Fri, 10 Dec 2021 11:21:04: 2000000 INFO @ Fri, 10 Dec 2021 11:21:10: 3000000 INFO @ Fri, 10 Dec 2021 11:21:16: 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 11:21:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.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 11:21:21: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:21:21: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:21:22: 5000000 INFO @ Fri, 10 Dec 2021 11:21:28: 1000000 INFO @ Fri, 10 Dec 2021 11:21:29: 6000000 INFO @ Fri, 10 Dec 2021 11:21:30: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:21:30: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:21:30: #1 total tags in treatment: 6218668 INFO @ Fri, 10 Dec 2021 11:21:30: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:21:30: #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 11:21:30: #1 tags after filtering in treatment: 6218668 INFO @ Fri, 10 Dec 2021 11:21:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:21:30: #1 finished! INFO @ Fri, 10 Dec 2021 11:21:30: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:21:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:21:31: #2 number of paired peaks: 413 WARNING @ Fri, 10 Dec 2021 11:21:31: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Fri, 10 Dec 2021 11:21:31: start model_add_line... INFO @ Fri, 10 Dec 2021 11:21:31: start X-correlation... INFO @ Fri, 10 Dec 2021 11:21:31: end of X-cor INFO @ Fri, 10 Dec 2021 11:21:31: #2 finished! INFO @ Fri, 10 Dec 2021 11:21:31: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Dec 2021 11:21:31: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 10 Dec 2021 11:21:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.05_model.r WARNING @ Fri, 10 Dec 2021 11:21:31: #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 11:21:31: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 10 Dec 2021 11:21:31: #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 11:21:31: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:21:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:21:33: 2000000 INFO @ Fri, 10 Dec 2021 11:21:39: 3000000 INFO @ Fri, 10 Dec 2021 11:21:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:21:45: 4000000 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 11:21:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:21:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:21:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.05_summits.bed INFO @ Fri, 10 Dec 2021 11:21:50: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1436 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:21:50: 5000000 INFO @ Fri, 10 Dec 2021 11:21:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.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 11:21:51: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:21:51: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:21:56: 6000000 INFO @ Fri, 10 Dec 2021 11:21:57: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:21:57: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:21:57: #1 total tags in treatment: 6218668 INFO @ Fri, 10 Dec 2021 11:21:57: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:21:57: #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 11:21:57: 1000000 INFO @ Fri, 10 Dec 2021 11:21:57: #1 tags after filtering in treatment: 6218668 INFO @ Fri, 10 Dec 2021 11:21:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:21:57: #1 finished! INFO @ Fri, 10 Dec 2021 11:21:57: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:21:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:21:58: #2 number of paired peaks: 413 WARNING @ Fri, 10 Dec 2021 11:21:58: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Fri, 10 Dec 2021 11:21:58: start model_add_line... INFO @ Fri, 10 Dec 2021 11:21:58: start X-correlation... INFO @ Fri, 10 Dec 2021 11:21:58: end of X-cor INFO @ Fri, 10 Dec 2021 11:21:58: #2 finished! INFO @ Fri, 10 Dec 2021 11:21:58: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Dec 2021 11:21:58: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 10 Dec 2021 11:21:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.10_model.r WARNING @ Fri, 10 Dec 2021 11:21:58: #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 11:21:58: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 10 Dec 2021 11:21:58: #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 11:21:58: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:21:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:22:03: 2000000 INFO @ Fri, 10 Dec 2021 11:22:09: 3000000 INFO @ Fri, 10 Dec 2021 11:22:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:22:14: 4000000 INFO @ Fri, 10 Dec 2021 11:22:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:22:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:22:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.10_summits.bed INFO @ Fri, 10 Dec 2021 11:22:17: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (1235 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:22:19: 5000000 INFO @ Fri, 10 Dec 2021 11:22:24: 6000000 INFO @ Fri, 10 Dec 2021 11:22:26: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:22:26: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:22:26: #1 total tags in treatment: 6218668 INFO @ Fri, 10 Dec 2021 11:22:26: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:22:26: #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 11:22:26: #1 tags after filtering in treatment: 6218668 INFO @ Fri, 10 Dec 2021 11:22:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:22:26: #1 finished! INFO @ Fri, 10 Dec 2021 11:22:26: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:22:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:22:26: #2 number of paired peaks: 413 WARNING @ Fri, 10 Dec 2021 11:22:26: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Fri, 10 Dec 2021 11:22:26: start model_add_line... INFO @ Fri, 10 Dec 2021 11:22:26: start X-correlation... INFO @ Fri, 10 Dec 2021 11:22:26: end of X-cor INFO @ Fri, 10 Dec 2021 11:22:26: #2 finished! INFO @ Fri, 10 Dec 2021 11:22:26: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Dec 2021 11:22:26: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 10 Dec 2021 11:22:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.20_model.r WARNING @ Fri, 10 Dec 2021 11:22:26: #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 11:22:26: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 10 Dec 2021 11:22:26: #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 11:22:26: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:22:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:22:39: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:22:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:22:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:22:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688910/SRX8688910.20_summits.bed INFO @ Fri, 10 Dec 2021 11:22:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (926 records, 4 fields): 2 millis CompletedMACS2peakCalling