Job ID = 6527786 SRX = SRX287590 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:43:40 prefetch.2.10.7: 1) Downloading 'SRR869733'... 2020-06-29T13:43:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:49:20 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:49:20 prefetch.2.10.7: 1) 'SRR869733' was downloaded successfully Read 19172821 spots for SRR869733/SRR869733.sra Written 19172821 spots for SRR869733/SRR869733.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: 00:07:53 19172821 reads; of these: 19172821 (100.00%) were unpaired; of these: 728054 (3.80%) aligned 0 times 12514383 (65.27%) aligned exactly 1 time 5930384 (30.93%) aligned >1 times 96.20% overall alignment rate Time searching: 00:07:53 Overall time: 00:07:53 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] 2855009 / 18444767 = 0.1548 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 23:07:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.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 23:07:56: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:07:56: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:08:02: 1000000 INFO @ Mon, 29 Jun 2020 23:08:09: 2000000 INFO @ Mon, 29 Jun 2020 23:08:16: 3000000 INFO @ Mon, 29 Jun 2020 23:08:23: 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 @ Mon, 29 Jun 2020 23:08:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.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 23:08:26: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:08:26: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:08:30: 5000000 INFO @ Mon, 29 Jun 2020 23:08:32: 1000000 INFO @ Mon, 29 Jun 2020 23:08:38: 2000000 INFO @ Mon, 29 Jun 2020 23:08:38: 6000000 INFO @ Mon, 29 Jun 2020 23:08:44: 3000000 INFO @ Mon, 29 Jun 2020 23:08:45: 7000000 INFO @ Mon, 29 Jun 2020 23:08:50: 4000000 INFO @ Mon, 29 Jun 2020 23:08:53: 8000000 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 23:08:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.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 23:08:56: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:08:56: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:08:56: 5000000 INFO @ Mon, 29 Jun 2020 23:09:00: 9000000 INFO @ Mon, 29 Jun 2020 23:09:02: 1000000 INFO @ Mon, 29 Jun 2020 23:09:03: 6000000 INFO @ Mon, 29 Jun 2020 23:09:08: 10000000 INFO @ Mon, 29 Jun 2020 23:09:09: 2000000 INFO @ Mon, 29 Jun 2020 23:09:09: 7000000 INFO @ Mon, 29 Jun 2020 23:09:15: 8000000 INFO @ Mon, 29 Jun 2020 23:09:15: 3000000 INFO @ Mon, 29 Jun 2020 23:09:15: 11000000 INFO @ Mon, 29 Jun 2020 23:09:21: 9000000 INFO @ Mon, 29 Jun 2020 23:09:22: 4000000 INFO @ Mon, 29 Jun 2020 23:09:23: 12000000 INFO @ Mon, 29 Jun 2020 23:09:28: 10000000 INFO @ Mon, 29 Jun 2020 23:09:28: 5000000 INFO @ Mon, 29 Jun 2020 23:09:31: 13000000 INFO @ Mon, 29 Jun 2020 23:09:34: 11000000 INFO @ Mon, 29 Jun 2020 23:09:35: 6000000 INFO @ Mon, 29 Jun 2020 23:09:38: 14000000 INFO @ Mon, 29 Jun 2020 23:09:40: 12000000 INFO @ Mon, 29 Jun 2020 23:09:41: 7000000 INFO @ Mon, 29 Jun 2020 23:09:45: 15000000 INFO @ Mon, 29 Jun 2020 23:09:46: 13000000 INFO @ Mon, 29 Jun 2020 23:09:48: 8000000 INFO @ Mon, 29 Jun 2020 23:09:49: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:09:49: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:09:49: #1 total tags in treatment: 15589758 INFO @ Mon, 29 Jun 2020 23:09:49: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:09:49: #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 23:09:49: #1 tags after filtering in treatment: 15589758 INFO @ Mon, 29 Jun 2020 23:09:49: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:09:49: #1 finished! INFO @ Mon, 29 Jun 2020 23:09:49: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:09:49: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:09:50: #2 number of paired peaks: 244 WARNING @ Mon, 29 Jun 2020 23:09:50: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Mon, 29 Jun 2020 23:09:50: start model_add_line... INFO @ Mon, 29 Jun 2020 23:09:50: start X-correlation... INFO @ Mon, 29 Jun 2020 23:09:50: end of X-cor INFO @ Mon, 29 Jun 2020 23:09:50: #2 finished! INFO @ Mon, 29 Jun 2020 23:09:50: #2 predicted fragment length is 46 bps INFO @ Mon, 29 Jun 2020 23:09:50: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 29 Jun 2020 23:09:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.05_model.r WARNING @ Mon, 29 Jun 2020 23:09:50: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:09:50: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 29 Jun 2020 23:09:50: #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 23:09:50: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:09:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:09:52: 14000000 INFO @ Mon, 29 Jun 2020 23:09:54: 9000000 INFO @ Mon, 29 Jun 2020 23:09:59: 15000000 INFO @ Mon, 29 Jun 2020 23:10:00: 10000000 INFO @ Mon, 29 Jun 2020 23:10:02: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:10:02: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:10:02: #1 total tags in treatment: 15589758 INFO @ Mon, 29 Jun 2020 23:10:02: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:10:02: #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 23:10:02: #1 tags after filtering in treatment: 15589758 INFO @ Mon, 29 Jun 2020 23:10:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:10:02: #1 finished! INFO @ Mon, 29 Jun 2020 23:10:02: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:10:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:10:04: #2 number of paired peaks: 244 WARNING @ Mon, 29 Jun 2020 23:10:04: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Mon, 29 Jun 2020 23:10:04: start model_add_line... INFO @ Mon, 29 Jun 2020 23:10:04: start X-correlation... INFO @ Mon, 29 Jun 2020 23:10:04: end of X-cor INFO @ Mon, 29 Jun 2020 23:10:04: #2 finished! INFO @ Mon, 29 Jun 2020 23:10:04: #2 predicted fragment length is 46 bps INFO @ Mon, 29 Jun 2020 23:10:04: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 29 Jun 2020 23:10:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.10_model.r WARNING @ Mon, 29 Jun 2020 23:10:04: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:10:04: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 29 Jun 2020 23:10:04: #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 23:10:04: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:10:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:10:06: 11000000 INFO @ Mon, 29 Jun 2020 23:10:12: 12000000 INFO @ Mon, 29 Jun 2020 23:10:18: 13000000 INFO @ Mon, 29 Jun 2020 23:10:24: 14000000 INFO @ Mon, 29 Jun 2020 23:10:25: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:10:30: 15000000 INFO @ Mon, 29 Jun 2020 23:10:33: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:10:33: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:10:33: #1 total tags in treatment: 15589758 INFO @ Mon, 29 Jun 2020 23:10:33: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:10:33: #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 23:10:33: #1 tags after filtering in treatment: 15589758 INFO @ Mon, 29 Jun 2020 23:10:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:10:33: #1 finished! INFO @ Mon, 29 Jun 2020 23:10:33: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:10:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:10:35: #2 number of paired peaks: 244 WARNING @ Mon, 29 Jun 2020 23:10:35: Fewer paired peaks (244) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 244 pairs to build model! INFO @ Mon, 29 Jun 2020 23:10:35: start model_add_line... INFO @ Mon, 29 Jun 2020 23:10:35: start X-correlation... INFO @ Mon, 29 Jun 2020 23:10:35: end of X-cor INFO @ Mon, 29 Jun 2020 23:10:35: #2 finished! INFO @ Mon, 29 Jun 2020 23:10:35: #2 predicted fragment length is 46 bps INFO @ Mon, 29 Jun 2020 23:10:35: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 29 Jun 2020 23:10:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.20_model.r WARNING @ Mon, 29 Jun 2020 23:10:35: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:10:35: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 29 Jun 2020 23:10:35: #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 23:10:35: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:10:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:10:36: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:10:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:10:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:10:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.05_summits.bed INFO @ Mon, 29 Jun 2020 23:10:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1955 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:10:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:10:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:10:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.10_summits.bed INFO @ Mon, 29 Jun 2020 23:10:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1635 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:11:06: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:11:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:11:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:11:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287590/SRX287590.20_summits.bed INFO @ Mon, 29 Jun 2020 23:11:23: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1267 records, 4 fields): 3 millis CompletedMACS2peakCalling