Job ID = 6455455 SRX = SRX287800 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:02:59 prefetch.2.10.7: 1) Downloading 'SRR869989'... 2020-06-21T10:02:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:04:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:04:39 prefetch.2.10.7: 'SRR869989' is valid 2020-06-21T10:04:39 prefetch.2.10.7: 1) 'SRR869989' was downloaded successfully Read 13055201 spots for SRR869989/SRR869989.sra Written 13055201 spots for SRR869989/SRR869989.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: 00:03:38 13055201 reads; of these: 13055201 (100.00%) were unpaired; of these: 906836 (6.95%) aligned 0 times 8499176 (65.10%) aligned exactly 1 time 3649189 (27.95%) aligned >1 times 93.05% overall alignment rate Time searching: 00:03:38 Overall time: 00:03:38 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] 1664202 / 12148365 = 0.1370 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 @ Sun, 21 Jun 2020 19:12:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.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 @ Sun, 21 Jun 2020 19:12:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:12:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:12:31: 1000000 INFO @ Sun, 21 Jun 2020 19:12:36: 2000000 INFO @ Sun, 21 Jun 2020 19:12:41: 3000000 INFO @ Sun, 21 Jun 2020 19:12:46: 4000000 INFO @ Sun, 21 Jun 2020 19:12:51: 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 @ Sun, 21 Jun 2020 19:12:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.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 @ Sun, 21 Jun 2020 19:12:55: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:12:55: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:12:56: 6000000 INFO @ Sun, 21 Jun 2020 19:13:01: 1000000 INFO @ Sun, 21 Jun 2020 19:13:02: 7000000 INFO @ Sun, 21 Jun 2020 19:13:06: 2000000 INFO @ Sun, 21 Jun 2020 19:13:07: 8000000 INFO @ Sun, 21 Jun 2020 19:13:12: 3000000 INFO @ Sun, 21 Jun 2020 19:13:13: 9000000 INFO @ Sun, 21 Jun 2020 19:13:17: 4000000 INFO @ Sun, 21 Jun 2020 19:13:18: 10000000 INFO @ Sun, 21 Jun 2020 19:13:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:13:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:13:21: #1 total tags in treatment: 10484163 INFO @ Sun, 21 Jun 2020 19:13:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:13:21: #1 tags after filtering in treatment: 10484162 INFO @ Sun, 21 Jun 2020 19:13:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:21: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:22: #2 number of paired peaks: 942 WARNING @ Sun, 21 Jun 2020 19:13:22: Fewer paired peaks (942) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 942 pairs to build model! INFO @ Sun, 21 Jun 2020 19:13:22: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:22: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:22: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:22: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:22: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 19:13:22: #2 alternative fragment length(s) may be 3,45 bps INFO @ Sun, 21 Jun 2020 19:13:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.05_model.r WARNING @ Sun, 21 Jun 2020 19:13:22: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:13:22: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Sun, 21 Jun 2020 19:13:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:13:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:13:22: 5000000 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 @ Sun, 21 Jun 2020 19:13:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.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 @ Sun, 21 Jun 2020 19:13:25: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:13:25: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:13:28: 6000000 INFO @ Sun, 21 Jun 2020 19:13:32: 1000000 INFO @ Sun, 21 Jun 2020 19:13:33: 7000000 INFO @ Sun, 21 Jun 2020 19:13:38: 2000000 INFO @ Sun, 21 Jun 2020 19:13:39: 8000000 INFO @ Sun, 21 Jun 2020 19:13:43: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:13:44: 3000000 INFO @ Sun, 21 Jun 2020 19:13:45: 9000000 INFO @ Sun, 21 Jun 2020 19:13:50: 10000000 INFO @ Sun, 21 Jun 2020 19:13:50: 4000000 INFO @ Sun, 21 Jun 2020 19:13:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:13:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:13:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.05_summits.bed INFO @ Sun, 21 Jun 2020 19:13:53: Done! pass1 - making usageList (525 chroms): 1 millis pass2 - checking and writing primary data (1761 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:13:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:13:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:13:53: #1 total tags in treatment: 10484163 INFO @ Sun, 21 Jun 2020 19:13:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:13:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:13:54: #1 tags after filtering in treatment: 10484162 INFO @ Sun, 21 Jun 2020 19:13:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:13:54: #1 finished! INFO @ Sun, 21 Jun 2020 19:13:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:13:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:13:55: #2 number of paired peaks: 942 WARNING @ Sun, 21 Jun 2020 19:13:55: Fewer paired peaks (942) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 942 pairs to build model! INFO @ Sun, 21 Jun 2020 19:13:55: start model_add_line... INFO @ Sun, 21 Jun 2020 19:13:55: start X-correlation... INFO @ Sun, 21 Jun 2020 19:13:55: end of X-cor INFO @ Sun, 21 Jun 2020 19:13:55: #2 finished! INFO @ Sun, 21 Jun 2020 19:13:55: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 19:13:55: #2 alternative fragment length(s) may be 3,45 bps INFO @ Sun, 21 Jun 2020 19:13:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.10_model.r WARNING @ Sun, 21 Jun 2020 19:13:55: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:13:55: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Sun, 21 Jun 2020 19:13:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:13:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:13:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:13:57: 5000000 INFO @ Sun, 21 Jun 2020 19:14:03: 6000000 INFO @ Sun, 21 Jun 2020 19:14:09: 7000000 INFO @ Sun, 21 Jun 2020 19:14:15: 8000000 INFO @ Sun, 21 Jun 2020 19:14:16: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:14:21: 9000000 INFO @ Sun, 21 Jun 2020 19:14:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:14:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:14:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.10_summits.bed INFO @ Sun, 21 Jun 2020 19:14:25: Done! pass1 - making usageList (475 chroms): 1 millis pass2 - checking and writing primary data (1716 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:14:27: 10000000 INFO @ Sun, 21 Jun 2020 19:14:30: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:14:30: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:14:30: #1 total tags in treatment: 10484163 INFO @ Sun, 21 Jun 2020 19:14:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:14:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:14:30: #1 tags after filtering in treatment: 10484162 INFO @ Sun, 21 Jun 2020 19:14:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:14:30: #1 finished! INFO @ Sun, 21 Jun 2020 19:14:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:14:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:14:31: #2 number of paired peaks: 942 WARNING @ Sun, 21 Jun 2020 19:14:31: Fewer paired peaks (942) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 942 pairs to build model! INFO @ Sun, 21 Jun 2020 19:14:31: start model_add_line... INFO @ Sun, 21 Jun 2020 19:14:31: start X-correlation... INFO @ Sun, 21 Jun 2020 19:14:31: end of X-cor INFO @ Sun, 21 Jun 2020 19:14:31: #2 finished! INFO @ Sun, 21 Jun 2020 19:14:31: #2 predicted fragment length is 45 bps INFO @ Sun, 21 Jun 2020 19:14:31: #2 alternative fragment length(s) may be 3,45 bps INFO @ Sun, 21 Jun 2020 19:14:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.20_model.r WARNING @ Sun, 21 Jun 2020 19:14:31: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:14:31: #2 You may need to consider one of the other alternative d(s): 3,45 WARNING @ Sun, 21 Jun 2020 19:14:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:14:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:14:31: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:14:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:15:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:15:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:15:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287800/SRX287800.20_summits.bed INFO @ Sun, 21 Jun 2020 19:15:02: Done! pass1 - making usageList (400 chroms): 1 millis pass2 - checking and writing primary data (1229 records, 4 fields): 13 millis CompletedMACS2peakCalling