Job ID = 6528148 SRX = SRX481091 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T14:26:21 prefetch.2.10.7: 1) Downloading 'SRR1182702'... 2020-06-29T14:26:21 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T14:29:45 prefetch.2.10.7: HTTPS download succeed 2020-06-29T14:29:45 prefetch.2.10.7: 1) 'SRR1182702' was downloaded successfully Read 19172821 spots for SRR1182702/SRR1182702.sra Written 19172821 spots for SRR1182702/SRR1182702.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: 00:07:17 19172821 reads; of these: 19172821 (100.00%) were unpaired; of these: 728026 (3.80%) aligned 0 times 12514312 (65.27%) aligned exactly 1 time 5930483 (30.93%) aligned >1 times 96.20% overall alignment rate Time searching: 00:07:17 Overall time: 00:07:17 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] 2855299 / 18444795 = 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 23:46:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.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 23:46:59: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:46:59: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:47:04: 1000000 INFO @ Mon, 29 Jun 2020 23:47:09: 2000000 INFO @ Mon, 29 Jun 2020 23:47:14: 3000000 INFO @ Mon, 29 Jun 2020 23:47:20: 4000000 INFO @ Mon, 29 Jun 2020 23:47:25: 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 23:47:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.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 23:47:29: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:47:29: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:47:30: 6000000 INFO @ Mon, 29 Jun 2020 23:47:35: 1000000 INFO @ Mon, 29 Jun 2020 23:47:36: 7000000 INFO @ Mon, 29 Jun 2020 23:47:41: 2000000 INFO @ Mon, 29 Jun 2020 23:47:42: 8000000 INFO @ Mon, 29 Jun 2020 23:47:46: 3000000 INFO @ Mon, 29 Jun 2020 23:47:47: 9000000 INFO @ Mon, 29 Jun 2020 23:47:52: 4000000 INFO @ Mon, 29 Jun 2020 23:47:53: 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 23:47:58: 5000000 INFO @ Mon, 29 Jun 2020 23:47:59: 11000000 INFO @ Mon, 29 Jun 2020 23:47:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.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 23:47:59: #1 read tag files... INFO @ Mon, 29 Jun 2020 23:47:59: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 23:48:04: 6000000 INFO @ Mon, 29 Jun 2020 23:48:05: 12000000 INFO @ Mon, 29 Jun 2020 23:48:05: 1000000 INFO @ Mon, 29 Jun 2020 23:48:09: 7000000 INFO @ Mon, 29 Jun 2020 23:48:10: 13000000 INFO @ Mon, 29 Jun 2020 23:48:11: 2000000 INFO @ Mon, 29 Jun 2020 23:48:15: 8000000 INFO @ Mon, 29 Jun 2020 23:48:16: 14000000 INFO @ Mon, 29 Jun 2020 23:48:17: 3000000 INFO @ Mon, 29 Jun 2020 23:48:21: 9000000 INFO @ Mon, 29 Jun 2020 23:48:22: 15000000 INFO @ Mon, 29 Jun 2020 23:48:23: 4000000 INFO @ Mon, 29 Jun 2020 23:48:26: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:48:26: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:48:26: #1 total tags in treatment: 15589496 INFO @ Mon, 29 Jun 2020 23:48:26: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:48:26: #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 23:48:26: #1 tags after filtering in treatment: 15589496 INFO @ Mon, 29 Jun 2020 23:48:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:48:26: #1 finished! INFO @ Mon, 29 Jun 2020 23:48:26: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:48:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:48:27: 10000000 INFO @ Mon, 29 Jun 2020 23:48:27: #2 number of paired peaks: 246 WARNING @ Mon, 29 Jun 2020 23:48:27: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Mon, 29 Jun 2020 23:48:27: start model_add_line... INFO @ Mon, 29 Jun 2020 23:48:27: start X-correlation... INFO @ Mon, 29 Jun 2020 23:48:27: end of X-cor INFO @ Mon, 29 Jun 2020 23:48:27: #2 finished! INFO @ Mon, 29 Jun 2020 23:48:27: #2 predicted fragment length is 43 bps INFO @ Mon, 29 Jun 2020 23:48:27: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 29 Jun 2020 23:48:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.05_model.r WARNING @ Mon, 29 Jun 2020 23:48:27: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:48:27: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 29 Jun 2020 23:48:27: #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 23:48:27: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:48:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:48:29: 5000000 INFO @ Mon, 29 Jun 2020 23:48:32: 11000000 INFO @ Mon, 29 Jun 2020 23:48:35: 6000000 INFO @ Mon, 29 Jun 2020 23:48:38: 12000000 INFO @ Mon, 29 Jun 2020 23:48:40: 7000000 INFO @ Mon, 29 Jun 2020 23:48:44: 13000000 INFO @ Mon, 29 Jun 2020 23:48:46: 8000000 INFO @ Mon, 29 Jun 2020 23:48:49: 14000000 INFO @ Mon, 29 Jun 2020 23:48:52: 9000000 INFO @ Mon, 29 Jun 2020 23:48:55: 15000000 INFO @ Mon, 29 Jun 2020 23:48:57: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:48:57: 10000000 INFO @ Mon, 29 Jun 2020 23:48:58: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:48:58: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:48:58: #1 total tags in treatment: 15589496 INFO @ Mon, 29 Jun 2020 23:48:58: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:48:58: #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 23:48:59: #1 tags after filtering in treatment: 15589496 INFO @ Mon, 29 Jun 2020 23:48:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:48:59: #1 finished! INFO @ Mon, 29 Jun 2020 23:48:59: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:48:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:49:00: #2 number of paired peaks: 246 WARNING @ Mon, 29 Jun 2020 23:49:00: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Mon, 29 Jun 2020 23:49:00: start model_add_line... INFO @ Mon, 29 Jun 2020 23:49:00: start X-correlation... INFO @ Mon, 29 Jun 2020 23:49:00: end of X-cor INFO @ Mon, 29 Jun 2020 23:49:00: #2 finished! INFO @ Mon, 29 Jun 2020 23:49:00: #2 predicted fragment length is 43 bps INFO @ Mon, 29 Jun 2020 23:49:00: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 29 Jun 2020 23:49:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.10_model.r WARNING @ Mon, 29 Jun 2020 23:49:00: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:49:00: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 29 Jun 2020 23:49:00: #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 23:49:00: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:49:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:49:03: 11000000 INFO @ Mon, 29 Jun 2020 23:49:08: 12000000 INFO @ Mon, 29 Jun 2020 23:49:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:49:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:49:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.05_summits.bed INFO @ Mon, 29 Jun 2020 23:49:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1981 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:49:13: 13000000 INFO @ Mon, 29 Jun 2020 23:49:19: 14000000 INFO @ Mon, 29 Jun 2020 23:49:24: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:49:27: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 23:49:27: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 23:49:27: #1 total tags in treatment: 15589496 INFO @ Mon, 29 Jun 2020 23:49:27: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:49:27: #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 23:49:27: #1 tags after filtering in treatment: 15589496 INFO @ Mon, 29 Jun 2020 23:49:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:49:27: #1 finished! INFO @ Mon, 29 Jun 2020 23:49:27: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:49:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:49:28: #2 number of paired peaks: 246 WARNING @ Mon, 29 Jun 2020 23:49:28: Fewer paired peaks (246) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 246 pairs to build model! INFO @ Mon, 29 Jun 2020 23:49:28: start model_add_line... INFO @ Mon, 29 Jun 2020 23:49:28: start X-correlation... INFO @ Mon, 29 Jun 2020 23:49:28: end of X-cor INFO @ Mon, 29 Jun 2020 23:49:28: #2 finished! INFO @ Mon, 29 Jun 2020 23:49:28: #2 predicted fragment length is 43 bps INFO @ Mon, 29 Jun 2020 23:49:28: #2 alternative fragment length(s) may be 43 bps INFO @ Mon, 29 Jun 2020 23:49:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.20_model.r WARNING @ Mon, 29 Jun 2020 23:49:28: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:49:28: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Mon, 29 Jun 2020 23:49:28: #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 23:49:28: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:49:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:49:30: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:49:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:49:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:49:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.10_summits.bed INFO @ Mon, 29 Jun 2020 23:49:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1672 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:49:57: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:50:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:50:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:50:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX481091/SRX481091.20_summits.bed INFO @ Mon, 29 Jun 2020 23:50:12: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1272 records, 4 fields): 2 millis CompletedMACS2peakCalling