Job ID = 6529876 SRX = SRX5343140 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:22 12114726 reads; of these: 12114726 (100.00%) were unpaired; of these: 661077 (5.46%) aligned 0 times 9790725 (80.82%) aligned exactly 1 time 1662924 (13.73%) aligned >1 times 94.54% overall alignment rate Time searching: 00:03:22 Overall time: 00:03:22 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1564806 / 11453649 = 0.1366 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:58:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.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, 30 Jun 2020 02:58:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:58:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:58:56: 1000000 INFO @ Tue, 30 Jun 2020 02:59:02: 2000000 INFO @ Tue, 30 Jun 2020 02:59:09: 3000000 INFO @ Tue, 30 Jun 2020 02:59:15: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:59:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.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, 30 Jun 2020 02:59:19: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:59:19: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:59:22: 5000000 INFO @ Tue, 30 Jun 2020 02:59:25: 1000000 INFO @ Tue, 30 Jun 2020 02:59:29: 6000000 INFO @ Tue, 30 Jun 2020 02:59:32: 2000000 INFO @ Tue, 30 Jun 2020 02:59:36: 7000000 INFO @ Tue, 30 Jun 2020 02:59:38: 3000000 INFO @ Tue, 30 Jun 2020 02:59:43: 8000000 INFO @ Tue, 30 Jun 2020 02:59:44: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 30 Jun 2020 02:59:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.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, 30 Jun 2020 02:59:49: #1 read tag files... INFO @ Tue, 30 Jun 2020 02:59:49: #1 read treatment tags... INFO @ Tue, 30 Jun 2020 02:59:50: 5000000 INFO @ Tue, 30 Jun 2020 02:59:50: 9000000 INFO @ Tue, 30 Jun 2020 02:59:56: 1000000 INFO @ Tue, 30 Jun 2020 02:59:56: 6000000 INFO @ Tue, 30 Jun 2020 02:59:56: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 02:59:56: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 02:59:56: #1 total tags in treatment: 9888843 INFO @ Tue, 30 Jun 2020 02:59:56: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 02:59:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 02:59:57: #1 tags after filtering in treatment: 9888835 INFO @ Tue, 30 Jun 2020 02:59:57: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 02:59:57: #1 finished! INFO @ Tue, 30 Jun 2020 02:59:57: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 02:59:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 02:59:57: #2 number of paired peaks: 161 WARNING @ Tue, 30 Jun 2020 02:59:57: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Tue, 30 Jun 2020 02:59:57: start model_add_line... INFO @ Tue, 30 Jun 2020 02:59:57: start X-correlation... INFO @ Tue, 30 Jun 2020 02:59:57: end of X-cor INFO @ Tue, 30 Jun 2020 02:59:57: #2 finished! INFO @ Tue, 30 Jun 2020 02:59:57: #2 predicted fragment length is 75 bps INFO @ Tue, 30 Jun 2020 02:59:57: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 30 Jun 2020 02:59:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.05_model.r WARNING @ Tue, 30 Jun 2020 02:59:57: #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, 30 Jun 2020 02:59:57: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Tue, 30 Jun 2020 02:59:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 02:59:57: #3 Call peaks... INFO @ Tue, 30 Jun 2020 02:59:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:00:02: 2000000 INFO @ Tue, 30 Jun 2020 03:00:02: 7000000 INFO @ Tue, 30 Jun 2020 03:00:08: 3000000 INFO @ Tue, 30 Jun 2020 03:00:08: 8000000 INFO @ Tue, 30 Jun 2020 03:00:14: 4000000 INFO @ Tue, 30 Jun 2020 03:00:15: 9000000 INFO @ Tue, 30 Jun 2020 03:00:17: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:00:20: 5000000 INFO @ Tue, 30 Jun 2020 03:00:21: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:00:21: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:00:21: #1 total tags in treatment: 9888843 INFO @ Tue, 30 Jun 2020 03:00:21: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:00:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:00:21: #1 tags after filtering in treatment: 9888835 INFO @ Tue, 30 Jun 2020 03:00:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:00:21: #1 finished! INFO @ Tue, 30 Jun 2020 03:00:21: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:00:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:00:22: #2 number of paired peaks: 161 WARNING @ Tue, 30 Jun 2020 03:00:22: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Tue, 30 Jun 2020 03:00:22: start model_add_line... INFO @ Tue, 30 Jun 2020 03:00:22: start X-correlation... INFO @ Tue, 30 Jun 2020 03:00:22: end of X-cor INFO @ Tue, 30 Jun 2020 03:00:22: #2 finished! INFO @ Tue, 30 Jun 2020 03:00:22: #2 predicted fragment length is 75 bps INFO @ Tue, 30 Jun 2020 03:00:22: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 30 Jun 2020 03:00:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.10_model.r WARNING @ Tue, 30 Jun 2020 03:00:22: #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, 30 Jun 2020 03:00:22: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Tue, 30 Jun 2020 03:00:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:00:22: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:00:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:00:26: 6000000 INFO @ Tue, 30 Jun 2020 03:00:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.05_peaks.xls INFO @ Tue, 30 Jun 2020 03:00:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.05_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:00:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.05_summits.bed INFO @ Tue, 30 Jun 2020 03:00:27: Done! pass1 - making usageList (242 chroms): 1 millis pass2 - checking and writing primary data (614 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 30 Jun 2020 03:00:31: 7000000 INFO @ Tue, 30 Jun 2020 03:00:37: 8000000 INFO @ Tue, 30 Jun 2020 03:00:42: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:00:43: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 30 Jun 2020 03:00:48: #1 tag size is determined as 65 bps INFO @ Tue, 30 Jun 2020 03:00:48: #1 tag size = 65 INFO @ Tue, 30 Jun 2020 03:00:48: #1 total tags in treatment: 9888843 INFO @ Tue, 30 Jun 2020 03:00:48: #1 user defined the maximum tags... INFO @ Tue, 30 Jun 2020 03:00:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 30 Jun 2020 03:00:48: #1 tags after filtering in treatment: 9888835 INFO @ Tue, 30 Jun 2020 03:00:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 30 Jun 2020 03:00:48: #1 finished! INFO @ Tue, 30 Jun 2020 03:00:48: #2 Build Peak Model... INFO @ Tue, 30 Jun 2020 03:00:48: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 30 Jun 2020 03:00:49: #2 number of paired peaks: 161 WARNING @ Tue, 30 Jun 2020 03:00:49: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Tue, 30 Jun 2020 03:00:49: start model_add_line... INFO @ Tue, 30 Jun 2020 03:00:49: start X-correlation... INFO @ Tue, 30 Jun 2020 03:00:49: end of X-cor INFO @ Tue, 30 Jun 2020 03:00:49: #2 finished! INFO @ Tue, 30 Jun 2020 03:00:49: #2 predicted fragment length is 75 bps INFO @ Tue, 30 Jun 2020 03:00:49: #2 alternative fragment length(s) may be 75 bps INFO @ Tue, 30 Jun 2020 03:00:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.20_model.r WARNING @ Tue, 30 Jun 2020 03:00:49: #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, 30 Jun 2020 03:00:49: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Tue, 30 Jun 2020 03:00:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 30 Jun 2020 03:00:49: #3 Call peaks... INFO @ Tue, 30 Jun 2020 03:00:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 30 Jun 2020 03:00:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.10_peaks.xls INFO @ Tue, 30 Jun 2020 03:00:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.10_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:00:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.10_summits.bed INFO @ Tue, 30 Jun 2020 03:00:52: Done! pass1 - making usageList (142 chroms): 0 millis pass2 - checking and writing primary data (295 records, 4 fields): 6 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 30 Jun 2020 03:01:10: #3 Call peaks for each chromosome... INFO @ Tue, 30 Jun 2020 03:01:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.20_peaks.xls INFO @ Tue, 30 Jun 2020 03:01:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.20_peaks.narrowPeak INFO @ Tue, 30 Jun 2020 03:01:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343140/SRX5343140.20_summits.bed INFO @ Tue, 30 Jun 2020 03:01:19: Done! pass1 - making usageList (90 chroms): 1 millis pass2 - checking and writing primary data (169 records, 4 fields): 4 millis CompletedMACS2peakCalling