Job ID = 6455667 SRX = SRX287972 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:19:51 prefetch.2.10.7: 1) Downloading 'SRR870161'... 2020-06-21T10:19:51 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:24:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:24:02 prefetch.2.10.7: 1) 'SRR870161' was downloaded successfully Read 17133552 spots for SRR870161/SRR870161.sra Written 17133552 spots for SRR870161/SRR870161.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: 00:05:25 17133552 reads; of these: 17133552 (100.00%) were unpaired; of these: 963545 (5.62%) aligned 0 times 11195675 (65.34%) aligned exactly 1 time 4974332 (29.03%) aligned >1 times 94.38% overall alignment rate Time searching: 00:05:25 Overall time: 00:05:25 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] 2735949 / 16170007 = 0.1692 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 19:34:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.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 19:34:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:34:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:34:40: 1000000 INFO @ Sun, 21 Jun 2020 19:34:46: 2000000 INFO @ Sun, 21 Jun 2020 19:34:51: 3000000 INFO @ Sun, 21 Jun 2020 19:34:56: 4000000 INFO @ Sun, 21 Jun 2020 19:35:02: 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 19:35:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.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 19:35:05: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:05: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:08: 6000000 INFO @ Sun, 21 Jun 2020 19:35:11: 1000000 INFO @ Sun, 21 Jun 2020 19:35:14: 7000000 INFO @ Sun, 21 Jun 2020 19:35:17: 2000000 INFO @ Sun, 21 Jun 2020 19:35:20: 8000000 INFO @ Sun, 21 Jun 2020 19:35:23: 3000000 INFO @ Sun, 21 Jun 2020 19:35:26: 9000000 INFO @ Sun, 21 Jun 2020 19:35:29: 4000000 INFO @ Sun, 21 Jun 2020 19:35:32: 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 @ Sun, 21 Jun 2020 19:35:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.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 19:35:35: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:35:35: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:35:35: 5000000 INFO @ Sun, 21 Jun 2020 19:35:38: 11000000 INFO @ Sun, 21 Jun 2020 19:35:41: 1000000 INFO @ Sun, 21 Jun 2020 19:35:41: 6000000 INFO @ Sun, 21 Jun 2020 19:35:44: 12000000 INFO @ Sun, 21 Jun 2020 19:35:47: 2000000 INFO @ Sun, 21 Jun 2020 19:35:48: 7000000 INFO @ Sun, 21 Jun 2020 19:35:51: 13000000 INFO @ Sun, 21 Jun 2020 19:35:53: 3000000 INFO @ Sun, 21 Jun 2020 19:35:54: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:35:54: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:35:54: #1 total tags in treatment: 13434058 INFO @ Sun, 21 Jun 2020 19:35:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:35:54: #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 19:35:54: 8000000 INFO @ Sun, 21 Jun 2020 19:35:54: #1 tags after filtering in treatment: 13434058 INFO @ Sun, 21 Jun 2020 19:35:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:35:54: #1 finished! INFO @ Sun, 21 Jun 2020 19:35:54: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:35:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:35:55: #2 number of paired peaks: 453 WARNING @ Sun, 21 Jun 2020 19:35:55: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Sun, 21 Jun 2020 19:35:55: start model_add_line... INFO @ Sun, 21 Jun 2020 19:35:55: start X-correlation... INFO @ Sun, 21 Jun 2020 19:35:55: end of X-cor INFO @ Sun, 21 Jun 2020 19:35:55: #2 finished! INFO @ Sun, 21 Jun 2020 19:35:55: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:35:55: #2 alternative fragment length(s) may be 4,39 bps INFO @ Sun, 21 Jun 2020 19:35:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.05_model.r WARNING @ Sun, 21 Jun 2020 19:35:55: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:35:55: #2 You may need to consider one of the other alternative d(s): 4,39 WARNING @ Sun, 21 Jun 2020 19:35:55: #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 19:35:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:35:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:35:59: 4000000 INFO @ Sun, 21 Jun 2020 19:36:00: 9000000 INFO @ Sun, 21 Jun 2020 19:36:05: 5000000 INFO @ Sun, 21 Jun 2020 19:36:07: 10000000 INFO @ Sun, 21 Jun 2020 19:36:11: 6000000 INFO @ Sun, 21 Jun 2020 19:36:13: 11000000 INFO @ Sun, 21 Jun 2020 19:36:18: 7000000 INFO @ Sun, 21 Jun 2020 19:36:20: 12000000 INFO @ Sun, 21 Jun 2020 19:36:22: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:24: 8000000 INFO @ Sun, 21 Jun 2020 19:36:26: 13000000 INFO @ Sun, 21 Jun 2020 19:36:29: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:36:29: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:36:29: #1 total tags in treatment: 13434058 INFO @ Sun, 21 Jun 2020 19:36:29: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:29: #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 19:36:29: #1 tags after filtering in treatment: 13434058 INFO @ Sun, 21 Jun 2020 19:36:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:29: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:30: 9000000 INFO @ Sun, 21 Jun 2020 19:36:30: #2 number of paired peaks: 453 WARNING @ Sun, 21 Jun 2020 19:36:30: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Sun, 21 Jun 2020 19:36:30: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:31: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:31: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:31: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:31: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:36:31: #2 alternative fragment length(s) may be 4,39 bps INFO @ Sun, 21 Jun 2020 19:36:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.10_model.r WARNING @ Sun, 21 Jun 2020 19:36:31: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:36:31: #2 You may need to consider one of the other alternative d(s): 4,39 WARNING @ Sun, 21 Jun 2020 19:36:31: #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 19:36:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:36:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:36:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:36:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.05_summits.bed INFO @ Sun, 21 Jun 2020 19:36:35: Done! pass1 - making usageList (611 chroms): 1 millis pass2 - checking and writing primary data (2492 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:36:36: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:36:42: 11000000 INFO @ Sun, 21 Jun 2020 19:36:48: 12000000 INFO @ Sun, 21 Jun 2020 19:36:54: 13000000 INFO @ Sun, 21 Jun 2020 19:36:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:36:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:36:56: #1 total tags in treatment: 13434058 INFO @ Sun, 21 Jun 2020 19:36:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:36:56: #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 19:36:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:36:57: #1 tags after filtering in treatment: 13434058 INFO @ Sun, 21 Jun 2020 19:36:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:36:57: #1 finished! INFO @ Sun, 21 Jun 2020 19:36:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:36:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:36:58: #2 number of paired peaks: 453 WARNING @ Sun, 21 Jun 2020 19:36:58: Fewer paired peaks (453) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 453 pairs to build model! INFO @ Sun, 21 Jun 2020 19:36:58: start model_add_line... INFO @ Sun, 21 Jun 2020 19:36:58: start X-correlation... INFO @ Sun, 21 Jun 2020 19:36:58: end of X-cor INFO @ Sun, 21 Jun 2020 19:36:58: #2 finished! INFO @ Sun, 21 Jun 2020 19:36:58: #2 predicted fragment length is 39 bps INFO @ Sun, 21 Jun 2020 19:36:58: #2 alternative fragment length(s) may be 4,39 bps INFO @ Sun, 21 Jun 2020 19:36:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.20_model.r WARNING @ Sun, 21 Jun 2020 19:36:58: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:36:58: #2 You may need to consider one of the other alternative d(s): 4,39 WARNING @ Sun, 21 Jun 2020 19:36:58: #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 19:36:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:36:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:37:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.10_summits.bed INFO @ Sun, 21 Jun 2020 19:37:10: Done! pass1 - making usageList (494 chroms): 1 millis pass2 - checking and writing primary data (1617 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:37:25: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:37:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:37:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:37:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX287972/SRX287972.20_summits.bed INFO @ Sun, 21 Jun 2020 19:37:38: Done! pass1 - making usageList (251 chroms): 1 millis pass2 - checking and writing primary data (514 records, 4 fields): 9 millis CompletedMACS2peakCalling