Job ID = 14167517 SRX = SRX8688958 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9126335 spots for SRR12174360/SRR12174360.sra Written 9126335 spots for SRR12174360/SRR12174360.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168085 ("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: 00:02:15 9126335 reads; of these: 9126335 (100.00%) were unpaired; of these: 3848766 (42.17%) aligned 0 times 3791870 (41.55%) aligned exactly 1 time 1485699 (16.28%) aligned >1 times 57.83% overall alignment rate Time searching: 00:02:15 Overall time: 00:02:15 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] 344794 / 5277569 = 0.0653 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 12:34:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.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 12:34:34: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:34:34: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:34:40: 1000000 INFO @ Fri, 10 Dec 2021 12:34:46: 2000000 INFO @ Fri, 10 Dec 2021 12:34:52: 3000000 INFO @ Fri, 10 Dec 2021 12:34:58: 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 12:35:03: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:35:03: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:35:03: #1 total tags in treatment: 4932775 INFO @ Fri, 10 Dec 2021 12:35:03: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:35:03: #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 12:35:03: #1 tags after filtering in treatment: 4932775 INFO @ Fri, 10 Dec 2021 12:35:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:35:03: #1 finished! INFO @ Fri, 10 Dec 2021 12:35:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:35:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:35:03: #2 number of paired peaks: 253 WARNING @ Fri, 10 Dec 2021 12:35:03: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Fri, 10 Dec 2021 12:35:03: start model_add_line... INFO @ Fri, 10 Dec 2021 12:35:04: start X-correlation... INFO @ Fri, 10 Dec 2021 12:35:04: end of X-cor INFO @ Fri, 10 Dec 2021 12:35:04: #2 finished! INFO @ Fri, 10 Dec 2021 12:35:04: #2 predicted fragment length is 51 bps INFO @ Fri, 10 Dec 2021 12:35:04: #2 alternative fragment length(s) may be 51 bps INFO @ Fri, 10 Dec 2021 12:35:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.05_model.r WARNING @ Fri, 10 Dec 2021 12:35:04: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:35:04: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Fri, 10 Dec 2021 12:35:04: #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 12:35:04: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:35:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:35:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.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 12:35:04: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:35:04: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:35:10: 1000000 INFO @ Fri, 10 Dec 2021 12:35:14: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:35:16: 2000000 INFO @ Fri, 10 Dec 2021 12:35:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.05_peaks.xls INFO @ Fri, 10 Dec 2021 12:35:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:35:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.05_summits.bed INFO @ Fri, 10 Dec 2021 12:35:19: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1044 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:35:22: 3000000 INFO @ Fri, 10 Dec 2021 12:35:27: 4000000 INFO @ Fri, 10 Dec 2021 12:35:32: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:35:32: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:35:32: #1 total tags in treatment: 4932775 INFO @ Fri, 10 Dec 2021 12:35:32: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:35:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) BedGraph に変換中... INFO @ Fri, 10 Dec 2021 12:35:33: #1 tags after filtering in treatment: 4932775 INFO @ Fri, 10 Dec 2021 12:35:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:35:33: #1 finished! INFO @ Fri, 10 Dec 2021 12:35:33: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:35:33: #2 looking for paired plus/minus strand peaks... 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 12:35:33: #2 number of paired peaks: 253 WARNING @ Fri, 10 Dec 2021 12:35:33: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Fri, 10 Dec 2021 12:35:33: start model_add_line... INFO @ Fri, 10 Dec 2021 12:35:33: start X-correlation... INFO @ Fri, 10 Dec 2021 12:35:33: end of X-cor INFO @ Fri, 10 Dec 2021 12:35:33: #2 finished! INFO @ Fri, 10 Dec 2021 12:35:33: #2 predicted fragment length is 51 bps INFO @ Fri, 10 Dec 2021 12:35:33: #2 alternative fragment length(s) may be 51 bps INFO @ Fri, 10 Dec 2021 12:35:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.10_model.r WARNING @ Fri, 10 Dec 2021 12:35:33: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:35:33: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Fri, 10 Dec 2021 12:35:33: #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 12:35:33: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:35:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 12:35:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.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 12:35:34: #1 read tag files... INFO @ Fri, 10 Dec 2021 12:35:34: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 12:35:40: 1000000 INFO @ Fri, 10 Dec 2021 12:35:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:35:46: 2000000 INFO @ Fri, 10 Dec 2021 12:35:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.10_peaks.xls INFO @ Fri, 10 Dec 2021 12:35:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:35:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.10_summits.bed INFO @ Fri, 10 Dec 2021 12:35:49: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (824 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 12:35:51: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 12:35:57: 4000000 INFO @ Fri, 10 Dec 2021 12:36:02: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 12:36:02: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 12:36:02: #1 total tags in treatment: 4932775 INFO @ Fri, 10 Dec 2021 12:36:02: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 12:36:02: #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 12:36:02: #1 tags after filtering in treatment: 4932775 INFO @ Fri, 10 Dec 2021 12:36:02: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 12:36:02: #1 finished! INFO @ Fri, 10 Dec 2021 12:36:02: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 12:36:02: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 12:36:03: #2 number of paired peaks: 253 WARNING @ Fri, 10 Dec 2021 12:36:03: Fewer paired peaks (253) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 253 pairs to build model! INFO @ Fri, 10 Dec 2021 12:36:03: start model_add_line... INFO @ Fri, 10 Dec 2021 12:36:03: start X-correlation... INFO @ Fri, 10 Dec 2021 12:36:03: end of X-cor INFO @ Fri, 10 Dec 2021 12:36:03: #2 finished! INFO @ Fri, 10 Dec 2021 12:36:03: #2 predicted fragment length is 51 bps INFO @ Fri, 10 Dec 2021 12:36:03: #2 alternative fragment length(s) may be 51 bps INFO @ Fri, 10 Dec 2021 12:36:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.20_model.r WARNING @ Fri, 10 Dec 2021 12:36:03: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 12:36:03: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Fri, 10 Dec 2021 12:36:03: #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 12:36:03: #3 Call peaks... INFO @ Fri, 10 Dec 2021 12:36:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 12:36:13: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 12:36:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.20_peaks.xls INFO @ Fri, 10 Dec 2021 12:36:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 12:36:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688958/SRX8688958.20_summits.bed INFO @ Fri, 10 Dec 2021 12:36:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (546 records, 4 fields): 1 millis CompletedMACS2peakCalling