Job ID = 16438040 SRX = SRX12261346 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20228104 spots for SRR15972602/SRR15972602.sra Written 20228104 spots for SRR15972602/SRR15972602.sra fastq に変換しました。 bowtie でマッピング中... Your job 16438137 ("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: 00:16:21 20228104 reads; of these: 20228104 (100.00%) were unpaired; of these: 861810 (4.26%) aligned 0 times 12456880 (61.58%) aligned exactly 1 time 6909414 (34.16%) aligned >1 times 95.74% overall alignment rate Time searching: 00:16:22 Overall time: 00:16:22 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_sort_core] merging from 8 files... [bam_rmdupse_core] 10408148 / 19366294 = 0.5374 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 13:46:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.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 13:46:33: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:46:33: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:46:44: 1000000 INFO @ Tue, 02 Aug 2022 13:46:55: 2000000 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 13:47:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.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 13:47:01: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:47:01: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:47:06: 3000000 INFO @ Tue, 02 Aug 2022 13:47:12: 1000000 INFO @ Tue, 02 Aug 2022 13:47:18: 4000000 INFO @ Tue, 02 Aug 2022 13:47:25: 2000000 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 13:47:30: 5000000 INFO @ Tue, 02 Aug 2022 13:47:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.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 13:47:33: #1 read tag files... INFO @ Tue, 02 Aug 2022 13:47:33: #1 read treatment tags... INFO @ Tue, 02 Aug 2022 13:47:39: 3000000 INFO @ Tue, 02 Aug 2022 13:47:44: 6000000 INFO @ Tue, 02 Aug 2022 13:47:48: 1000000 INFO @ Tue, 02 Aug 2022 13:47:52: 4000000 INFO @ Tue, 02 Aug 2022 13:47:56: 7000000 INFO @ Tue, 02 Aug 2022 13:48:03: 5000000 INFO @ Tue, 02 Aug 2022 13:48:03: 2000000 INFO @ Tue, 02 Aug 2022 13:48:09: 8000000 INFO @ Tue, 02 Aug 2022 13:48:16: 6000000 INFO @ Tue, 02 Aug 2022 13:48:19: 3000000 INFO @ Tue, 02 Aug 2022 13:48:22: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:48:22: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:48:22: #1 total tags in treatment: 8958146 INFO @ Tue, 02 Aug 2022 13:48:22: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:48:22: #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 13:48:22: #1 tags after filtering in treatment: 8958146 INFO @ Tue, 02 Aug 2022 13:48:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:48:22: #1 finished! INFO @ Tue, 02 Aug 2022 13:48:22: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:48:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:48:23: #2 number of paired peaks: 558 WARNING @ Tue, 02 Aug 2022 13:48:23: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Tue, 02 Aug 2022 13:48:23: start model_add_line... INFO @ Tue, 02 Aug 2022 13:48:23: start X-correlation... INFO @ Tue, 02 Aug 2022 13:48:23: end of X-cor INFO @ Tue, 02 Aug 2022 13:48:23: #2 finished! INFO @ Tue, 02 Aug 2022 13:48:23: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 13:48:23: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 02 Aug 2022 13:48:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.05_model.r WARNING @ Tue, 02 Aug 2022 13:48:23: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:48:23: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Tue, 02 Aug 2022 13:48:23: #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 13:48:23: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:48:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:48:29: 7000000 INFO @ Tue, 02 Aug 2022 13:48:33: 4000000 INFO @ Tue, 02 Aug 2022 13:48:40: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 02 Aug 2022 13:48:48: 5000000 INFO @ Tue, 02 Aug 2022 13:48:50: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:48:51: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:48:51: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:48:51: #1 total tags in treatment: 8958146 INFO @ Tue, 02 Aug 2022 13:48:51: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:48:51: #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 13:48:51: #1 tags after filtering in treatment: 8958146 INFO @ Tue, 02 Aug 2022 13:48:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:48:51: #1 finished! INFO @ Tue, 02 Aug 2022 13:48:51: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:48:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:48:52: #2 number of paired peaks: 558 WARNING @ Tue, 02 Aug 2022 13:48:52: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Tue, 02 Aug 2022 13:48:52: start model_add_line... INFO @ Tue, 02 Aug 2022 13:48:52: start X-correlation... INFO @ Tue, 02 Aug 2022 13:48:52: end of X-cor INFO @ Tue, 02 Aug 2022 13:48:52: #2 finished! INFO @ Tue, 02 Aug 2022 13:48:52: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 13:48:52: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 02 Aug 2022 13:48:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.10_model.r WARNING @ Tue, 02 Aug 2022 13:48:52: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:48:52: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Tue, 02 Aug 2022 13:48:52: #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 13:48:52: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:48:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:49:03: 6000000 INFO @ Tue, 02 Aug 2022 13:49:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.05_peaks.xls INFO @ Tue, 02 Aug 2022 13:49:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.05_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:49:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.05_summits.bed INFO @ Tue, 02 Aug 2022 13:49:05: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (7621 records, 4 fields): 38 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 02 Aug 2022 13:49:16: 7000000 INFO @ Tue, 02 Aug 2022 13:49:19: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:49:30: 8000000 INFO @ Tue, 02 Aug 2022 13:49:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.10_peaks.xls INFO @ Tue, 02 Aug 2022 13:49:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.10_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:49:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.10_summits.bed INFO @ Tue, 02 Aug 2022 13:49:34: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3183 records, 4 fields): 51 millis CompletedMACS2peakCalling INFO @ Tue, 02 Aug 2022 13:49:45: #1 tag size is determined as 74 bps INFO @ Tue, 02 Aug 2022 13:49:45: #1 tag size = 74 INFO @ Tue, 02 Aug 2022 13:49:45: #1 total tags in treatment: 8958146 INFO @ Tue, 02 Aug 2022 13:49:45: #1 user defined the maximum tags... INFO @ Tue, 02 Aug 2022 13:49:45: #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 13:49:45: #1 tags after filtering in treatment: 8958146 INFO @ Tue, 02 Aug 2022 13:49:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 02 Aug 2022 13:49:45: #1 finished! INFO @ Tue, 02 Aug 2022 13:49:45: #2 Build Peak Model... INFO @ Tue, 02 Aug 2022 13:49:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 02 Aug 2022 13:49:46: #2 number of paired peaks: 558 WARNING @ Tue, 02 Aug 2022 13:49:46: Fewer paired peaks (558) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 558 pairs to build model! INFO @ Tue, 02 Aug 2022 13:49:46: start model_add_line... INFO @ Tue, 02 Aug 2022 13:49:46: start X-correlation... INFO @ Tue, 02 Aug 2022 13:49:46: end of X-cor INFO @ Tue, 02 Aug 2022 13:49:46: #2 finished! INFO @ Tue, 02 Aug 2022 13:49:46: #2 predicted fragment length is 75 bps INFO @ Tue, 02 Aug 2022 13:49:46: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 02 Aug 2022 13:49:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.20_model.r WARNING @ Tue, 02 Aug 2022 13:49:46: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 02 Aug 2022 13:49:46: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Tue, 02 Aug 2022 13:49:46: #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 13:49:46: #3 Call peaks... INFO @ Tue, 02 Aug 2022 13:49:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 02 Aug 2022 13:50:13: #3 Call peaks for each chromosome... INFO @ Tue, 02 Aug 2022 13:50:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.20_peaks.xls INFO @ Tue, 02 Aug 2022 13:50:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.20_peaks.narrowPeak INFO @ Tue, 02 Aug 2022 13:50:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX12261346/SRX12261346.20_summits.bed INFO @ Tue, 02 Aug 2022 13:50:27: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (805 records, 4 fields): 131 millis CompletedMACS2peakCalling