Job ID = 6528149 SRX = SRX481092 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:29:32 prefetch.2.10.7: 1) Downloading 'SRR1182703'... 2020-06-29T14:29:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:33:53 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:33:53 prefetch.2.10.7: 1) 'SRR1182703' was downloaded successfully Read 22109731 spots for SRR1182703/SRR1182703.sra Written 22109731 spots for SRR1182703/SRR1182703.sra 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: 00:07:52 22109731 reads; of these: 22109731 (100.00%) were unpaired; of these: 1293844 (5.85%) aligned 0 times 13813279 (62.48%) aligned exactly 1 time 7002608 (31.67%) aligned >1 times 94.15% overall alignment rate Time searching: 00:07:52 Overall time: 00:07:52 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 12 files... [bam_rmdupse_core] 3520972 / 20815887 = 0.1691 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 @ Mon, 29 Jun 2020 23:52:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.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 @ Mon, 29 Jun 2020 23:52:45: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:52:45: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:52:51: 1000000 INFO @ Mon, 29 Jun 2020 23:52:56: 2000000 INFO @ Mon, 29 Jun 2020 23:53:02: 3000000 INFO @ Mon, 29 Jun 2020 23:53:07: 4000000 INFO @ Mon, 29 Jun 2020 23:53:13: 5000000 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 @ Mon, 29 Jun 2020 23:53:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.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 @ Mon, 29 Jun 2020 23:53:15: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:53:15: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:53:19: 6000000 INFO @ Mon, 29 Jun 2020 23:53:20: 1000000 INFO @ Mon, 29 Jun 2020 23:53:24: 7000000 INFO @ Mon, 29 Jun 2020 23:53:25: 2000000 INFO @ Mon, 29 Jun 2020 23:53:30: 8000000 INFO @ Mon, 29 Jun 2020 23:53:30: 3000000 INFO @ Mon, 29 Jun 2020 23:53:35: 4000000 INFO @ Mon, 29 Jun 2020 23:53:36: 9000000 INFO @ Mon, 29 Jun 2020 23:53:40: 5000000 INFO @ Mon, 29 Jun 2020 23:53:41: 10000000 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 @ Mon, 29 Jun 2020 23:53:45: 6000000 INFO @ Mon, 29 Jun 2020 23:53:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.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 @ Mon, 29 Jun 2020 23:53:45: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:53:45: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:53:47: 11000000 INFO @ Mon, 29 Jun 2020 23:53:50: 7000000 INFO @ Mon, 29 Jun 2020 23:53:50: 1000000 INFO @ Mon, 29 Jun 2020 23:53:53: 12000000 INFO @ Mon, 29 Jun 2020 23:53:55: 8000000 INFO @ Mon, 29 Jun 2020 23:53:55: 2000000 INFO @ Mon, 29 Jun 2020 23:53:59: 13000000 INFO @ Mon, 29 Jun 2020 23:54:00: 9000000 INFO @ Mon, 29 Jun 2020 23:54:00: 3000000 INFO @ Mon, 29 Jun 2020 23:54:04: 10000000 INFO @ Mon, 29 Jun 2020 23:54:05: 14000000 INFO @ Mon, 29 Jun 2020 23:54:05: 4000000 INFO @ Mon, 29 Jun 2020 23:54:09: 11000000 INFO @ Mon, 29 Jun 2020 23:54:10: 15000000 INFO @ Mon, 29 Jun 2020 23:54:10: 5000000 INFO @ Mon, 29 Jun 2020 23:54:14: 12000000 INFO @ Mon, 29 Jun 2020 23:54:15: 6000000 INFO @ Mon, 29 Jun 2020 23:54:16: 16000000 INFO @ Mon, 29 Jun 2020 23:54:19: 13000000 INFO @ Mon, 29 Jun 2020 23:54:20: 7000000 INFO @ Mon, 29 Jun 2020 23:54:21: 17000000 INFO @ Mon, 29 Jun 2020 23:54:23: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:54:23: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:54:23: #1 total tags in treatment: 17294915 INFO @ Mon, 29 Jun 2020 23:54:23: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:54:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:54:24: #1 tags after filtering in treatment: 17294915 INFO @ Mon, 29 Jun 2020 23:54:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:54:24: #1 finished! INFO @ Mon, 29 Jun 2020 23:54:24: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:54:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:54:24: 14000000 INFO @ Mon, 29 Jun 2020 23:54:25: #2 number of paired peaks: 195 WARNING @ Mon, 29 Jun 2020 23:54:25: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Mon, 29 Jun 2020 23:54:25: start model_add_line... INFO @ Mon, 29 Jun 2020 23:54:25: start X-correlation... INFO @ Mon, 29 Jun 2020 23:54:25: end of X-cor INFO @ Mon, 29 Jun 2020 23:54:25: #2 finished! INFO @ Mon, 29 Jun 2020 23:54:25: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 23:54:25: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 29 Jun 2020 23:54:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.05_model.r WARNING @ Mon, 29 Jun 2020 23:54:25: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:54:25: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 29 Jun 2020 23:54:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:54:25: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:54:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:54:25: 8000000 INFO @ Mon, 29 Jun 2020 23:54:29: 15000000 INFO @ Mon, 29 Jun 2020 23:54:30: 9000000 INFO @ Mon, 29 Jun 2020 23:54:34: 16000000 INFO @ Mon, 29 Jun 2020 23:54:35: 10000000 INFO @ Mon, 29 Jun 2020 23:54:39: 17000000 INFO @ Mon, 29 Jun 2020 23:54:40: 11000000 INFO @ Mon, 29 Jun 2020 23:54:41: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:54:41: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:54:41: #1 total tags in treatment: 17294915 INFO @ Mon, 29 Jun 2020 23:54:41: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:54:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:54:41: #1 tags after filtering in treatment: 17294915 INFO @ Mon, 29 Jun 2020 23:54:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:54:41: #1 finished! INFO @ Mon, 29 Jun 2020 23:54:41: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:54:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:54:42: #2 number of paired peaks: 195 WARNING @ Mon, 29 Jun 2020 23:54:42: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Mon, 29 Jun 2020 23:54:42: start model_add_line... INFO @ Mon, 29 Jun 2020 23:54:42: start X-correlation... INFO @ Mon, 29 Jun 2020 23:54:42: end of X-cor INFO @ Mon, 29 Jun 2020 23:54:42: #2 finished! INFO @ Mon, 29 Jun 2020 23:54:42: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 23:54:42: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 29 Jun 2020 23:54:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.10_model.r WARNING @ Mon, 29 Jun 2020 23:54:42: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:54:42: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 29 Jun 2020 23:54:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:54:42: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:54:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:54:45: 12000000 INFO @ Mon, 29 Jun 2020 23:54:50: 13000000 INFO @ Mon, 29 Jun 2020 23:54:55: 14000000 INFO @ Mon, 29 Jun 2020 23:54:56: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:55:00: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:55:05: 16000000 INFO @ Mon, 29 Jun 2020 23:55:10: 17000000 INFO @ Mon, 29 Jun 2020 23:55:11: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:55:11: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:55:11: #1 total tags in treatment: 17294915 INFO @ Mon, 29 Jun 2020 23:55:11: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:55:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 23:55:12: #1 tags after filtering in treatment: 17294915 INFO @ Mon, 29 Jun 2020 23:55:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:55:12: #1 finished! INFO @ Mon, 29 Jun 2020 23:55:12: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:55:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:55:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:55:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:55:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.05_summits.bed INFO @ Mon, 29 Jun 2020 23:55:13: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2227 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:55:13: #2 number of paired peaks: 195 WARNING @ Mon, 29 Jun 2020 23:55:13: Fewer paired peaks (195) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 195 pairs to build model! INFO @ Mon, 29 Jun 2020 23:55:13: start model_add_line... INFO @ Mon, 29 Jun 2020 23:55:13: start X-correlation... INFO @ Mon, 29 Jun 2020 23:55:13: end of X-cor INFO @ Mon, 29 Jun 2020 23:55:13: #2 finished! INFO @ Mon, 29 Jun 2020 23:55:13: #2 predicted fragment length is 47 bps INFO @ Mon, 29 Jun 2020 23:55:13: #2 alternative fragment length(s) may be 47 bps INFO @ Mon, 29 Jun 2020 23:55:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.20_model.r WARNING @ Mon, 29 Jun 2020 23:55:13: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:55:13: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Mon, 29 Jun 2020 23:55:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 23:55:13: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:55:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:55:13: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:55:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:55:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:55:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.10_summits.bed INFO @ Mon, 29 Jun 2020 23:55:30: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1791 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:55:46: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:56:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:56:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:56:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX481092/SRX481092.20_summits.bed INFO @ Mon, 29 Jun 2020 23:56:02: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1365 records, 4 fields): 3 millis CompletedMACS2peakCalling