Job ID = 16439191 SRX = SRX15206468 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-08-02T05:45:17 prefetch.2.10.7: 1) Downloading 'SRR19139338'... 2022-08-02T05:45:17 prefetch.2.10.7: Downloading via HTTPS... 2022-08-02T05:45:25 prefetch.2.10.7: HTTPS download succeed 2022-08-02T05:45:25 prefetch.2.10.7: 'SRR19139338' is valid 2022-08-02T05:45:25 prefetch.2.10.7: 1) 'SRR19139338' was downloaded successfully 2022-08-02T05:45:25 prefetch.2.10.7: 'SRR19139338' has 0 unresolved dependencies Read 5613954 spots for SRR19139338/SRR19139338.sra Written 5613954 spots for SRR19139338/SRR19139338.sra fastq に変換しました。 bowtie でマッピング中... Your job 16439286 ("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: 00:02:20 5613954 reads; of these: 5613954 (100.00%) were unpaired; of these: 130239 (2.32%) aligned 0 times 2513148 (44.77%) aligned exactly 1 time 2970567 (52.91%) aligned >1 times 97.68% overall alignment rate Time searching: 00:02:20 Overall time: 00:02:20 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] 549838 / 5483715 = 0.1003 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/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:49:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.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 @ Tue, 02 Aug 2022 14:49:36: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:49:36: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:49:42: 1000000 INFO @ Tue, 02 Aug 2022 14:49:47: 2000000 INFO @ Tue, 02 Aug 2022 14:49:52: 3000000 INFO @ Tue, 02 Aug 2022 14:49:58: 4000000 INFO @ Tue, 02 Aug 2022 14:50:03: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:50:03: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:50:03: #1 total tags in treatment: 4933877 INFO @ Tue, 02 Aug 2022 14:50:03: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:50:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:50:03: #1 tags after filtering in treatment: 4933877 INFO @ Tue, 02 Aug 2022 14:50:03: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:50:03: #1 finished! INFO @ Tue, 02 Aug 2022 14:50:03: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:50:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:50:03: #2 number of paired peaks: 874 WARNING @ Tue, 02 Aug 2022 14:50:03: Fewer paired peaks (874) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 874 pairs to build model! INFO @ Tue, 02 Aug 2022 14:50:03: start model_add_line... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:50:04: start X-correlation... INFO @ Tue, 02 Aug 2022 14:50:04: end of X-cor INFO @ Tue, 02 Aug 2022 14:50:04: #2 finished! INFO @ Tue, 02 Aug 2022 14:50:04: #2 predicted fragment length is 81 bps INFO @ Tue, 02 Aug 2022 14:50:04: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 02 Aug 2022 14:50:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.05_model.r WARNING @ Tue, 02 Aug 2022 14:50:04: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:50:04: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Tue, 02 Aug 2022 14:50:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:50:04: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:50:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:50:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.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 @ Tue, 02 Aug 2022 14:50:05: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:50:05: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:50:12: 1000000 INFO @ Tue, 02 Aug 2022 14:50:14: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:50:18: 2000000 INFO @ Tue, 02 Aug 2022 14:50:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.05_peaks.xls INFO @ Tue, 02 Aug 2022 14:50:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:50:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.05_summits.bed INFO @ Tue, 02 Aug 2022 14:50:20: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1529 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:50:24: 3000000 INFO @ Tue, 02 Aug 2022 14:50:30: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.7/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 02 Aug 2022 14:50:35: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:50:35: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:50:35: #1 total tags in treatment: 4933877 INFO @ Tue, 02 Aug 2022 14:50:35: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:50:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:50:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.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 @ Tue, 02 Aug 2022 14:50:35: #1 read tag files... INFO @ Tue, 02 Aug 2022 14:50:35: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 14:50:35: #1 tags after filtering in treatment: 4933877 INFO @ Tue, 02 Aug 2022 14:50:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:50:35: #1 finished! INFO @ Tue, 02 Aug 2022 14:50:35: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:50:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:50:36: #2 number of paired peaks: 874 WARNING @ Tue, 02 Aug 2022 14:50:36: Fewer paired peaks (874) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 874 pairs to build model! INFO @ Tue, 02 Aug 2022 14:50:36: start model_add_line... INFO @ Tue, 02 Aug 2022 14:50:36: start X-correlation... INFO @ Tue, 02 Aug 2022 14:50:36: end of X-cor INFO @ Tue, 02 Aug 2022 14:50:36: #2 finished! INFO @ Tue, 02 Aug 2022 14:50:36: #2 predicted fragment length is 81 bps INFO @ Tue, 02 Aug 2022 14:50:36: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 02 Aug 2022 14:50:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.10_model.r WARNING @ Tue, 02 Aug 2022 14:50:36: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:50:36: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Tue, 02 Aug 2022 14:50:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:50:36: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:50:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 14:50:41: 1000000 INFO @ Tue, 02 Aug 2022 14:50:46: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:50:48: 2000000 INFO @ Tue, 02 Aug 2022 14:50:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.10_peaks.xls INFO @ Tue, 02 Aug 2022 14:50:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:50:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.10_summits.bed INFO @ Tue, 02 Aug 2022 14:50:51: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (410 records, 4 fields): 314 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 14:50:54: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 14:51:00: 4000000 INFO @ Tue, 02 Aug 2022 14:51:05: #1 tag size is determined as 50 bps INFO @ Tue, 02 Aug 2022 14:51:05: #1 tag size = 50 INFO @ Tue, 02 Aug 2022 14:51:05: #1 total tags in treatment: 4933877 INFO @ Tue, 02 Aug 2022 14:51:05: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 14:51:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 02 Aug 2022 14:51:06: #1 tags after filtering in treatment: 4933877 INFO @ Tue, 02 Aug 2022 14:51:06: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 14:51:06: #1 finished! INFO @ Tue, 02 Aug 2022 14:51:06: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 14:51:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 14:51:06: #2 number of paired peaks: 874 WARNING @ Tue, 02 Aug 2022 14:51:06: Fewer paired peaks (874) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 874 pairs to build model! INFO @ Tue, 02 Aug 2022 14:51:06: start model_add_line... INFO @ Tue, 02 Aug 2022 14:51:06: start X-correlation... INFO @ Tue, 02 Aug 2022 14:51:06: end of X-cor INFO @ Tue, 02 Aug 2022 14:51:06: #2 finished! INFO @ Tue, 02 Aug 2022 14:51:06: #2 predicted fragment length is 81 bps INFO @ Tue, 02 Aug 2022 14:51:06: #2 alternative fragment length(s) may be 81 bps INFO @ Tue, 02 Aug 2022 14:51:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.20_model.r WARNING @ Tue, 02 Aug 2022 14:51:06: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 14:51:06: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Tue, 02 Aug 2022 14:51:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 02 Aug 2022 14:51:06: #3 Call peaks... INFO @ Tue, 02 Aug 2022 14:51:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 14:51:16: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 14:51:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.20_peaks.xls INFO @ Tue, 02 Aug 2022 14:51:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 14:51:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX15206468/SRX15206468.20_summits.bed INFO @ Tue, 02 Aug 2022 14:51:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (99 records, 4 fields): 14 millis CompletedMACS2peakCalling