Job ID = 6456914 SRX = SRX4053366 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:16:09 prefetch.2.10.7: 1) Downloading 'SRR7132347'... 2020-06-21T11:16:09 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:20:02 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:20:03 prefetch.2.10.7: 'SRR7132347' is valid 2020-06-21T11:20:03 prefetch.2.10.7: 1) 'SRR7132347' was downloaded successfully 2020-06-21T11:20:03 prefetch.2.10.7: 'SRR7132347' has 0 unresolved dependencies Read 28729221 spots for SRR7132347/SRR7132347.sra Written 28729221 spots for SRR7132347/SRR7132347.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: 00:10:18 28729221 reads; of these: 28729221 (100.00%) were unpaired; of these: 5858565 (20.39%) aligned 0 times 10785048 (37.54%) aligned exactly 1 time 12085608 (42.07%) aligned >1 times 79.61% overall alignment rate Time searching: 00:10:18 Overall time: 00:10:18 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 12 files... [bam_rmdupse_core] 11421177 / 22870656 = 0.4994 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 20:35:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.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 20:35:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:35:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:35:54: 1000000 INFO @ Sun, 21 Jun 2020 20:36:00: 2000000 INFO @ Sun, 21 Jun 2020 20:36:06: 3000000 INFO @ Sun, 21 Jun 2020 20:36:11: 4000000 INFO @ Sun, 21 Jun 2020 20:36:17: 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 20:36:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.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 20:36:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:36:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:36:23: 6000000 INFO @ Sun, 21 Jun 2020 20:36:25: 1000000 INFO @ Sun, 21 Jun 2020 20:36:29: 7000000 INFO @ Sun, 21 Jun 2020 20:36:31: 2000000 INFO @ Sun, 21 Jun 2020 20:36:35: 8000000 INFO @ Sun, 21 Jun 2020 20:36:37: 3000000 INFO @ Sun, 21 Jun 2020 20:36:41: 9000000 INFO @ Sun, 21 Jun 2020 20:36:43: 4000000 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 20:36:48: 10000000 INFO @ Sun, 21 Jun 2020 20:36:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.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 20:36:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:36:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:36:49: 5000000 INFO @ Sun, 21 Jun 2020 20:36:54: 11000000 INFO @ Sun, 21 Jun 2020 20:36:56: 6000000 INFO @ Sun, 21 Jun 2020 20:36:56: 1000000 INFO @ Sun, 21 Jun 2020 20:36:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:36:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:36:57: #1 total tags in treatment: 11449479 INFO @ Sun, 21 Jun 2020 20:36:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:36:57: #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 20:36:58: #1 tags after filtering in treatment: 11449476 INFO @ Sun, 21 Jun 2020 20:36:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:36:58: #1 finished! INFO @ Sun, 21 Jun 2020 20:36:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:36:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:36:59: #2 number of paired peaks: 789 WARNING @ Sun, 21 Jun 2020 20:36:59: Fewer paired peaks (789) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 789 pairs to build model! INFO @ Sun, 21 Jun 2020 20:36:59: start model_add_line... INFO @ Sun, 21 Jun 2020 20:36:59: start X-correlation... INFO @ Sun, 21 Jun 2020 20:36:59: end of X-cor INFO @ Sun, 21 Jun 2020 20:36:59: #2 finished! INFO @ Sun, 21 Jun 2020 20:36:59: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 20:36:59: #2 alternative fragment length(s) may be 4,47 bps INFO @ Sun, 21 Jun 2020 20:36:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.05_model.r WARNING @ Sun, 21 Jun 2020 20:36:59: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:36:59: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Sun, 21 Jun 2020 20:36:59: #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 20:36:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:36:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:37:03: 7000000 INFO @ Sun, 21 Jun 2020 20:37:04: 2000000 INFO @ Sun, 21 Jun 2020 20:37:10: 8000000 INFO @ Sun, 21 Jun 2020 20:37:11: 3000000 INFO @ Sun, 21 Jun 2020 20:37:17: 9000000 INFO @ Sun, 21 Jun 2020 20:37:19: 4000000 INFO @ Sun, 21 Jun 2020 20:37:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:37:24: 10000000 INFO @ Sun, 21 Jun 2020 20:37:27: 5000000 INFO @ Sun, 21 Jun 2020 20:37:31: 11000000 INFO @ Sun, 21 Jun 2020 20:37:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:37:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:37:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.05_summits.bed INFO @ Sun, 21 Jun 2020 20:37:32: Done! pass1 - making usageList (768 chroms): 1 millis pass2 - checking and writing primary data (3868 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:37:34: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:37:34: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:37:34: #1 total tags in treatment: 11449479 INFO @ Sun, 21 Jun 2020 20:37:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:37:34: #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 20:37:34: 6000000 INFO @ Sun, 21 Jun 2020 20:37:34: #1 tags after filtering in treatment: 11449476 INFO @ Sun, 21 Jun 2020 20:37:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:37:34: #1 finished! INFO @ Sun, 21 Jun 2020 20:37:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:37:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:37:35: #2 number of paired peaks: 789 WARNING @ Sun, 21 Jun 2020 20:37:35: Fewer paired peaks (789) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 789 pairs to build model! INFO @ Sun, 21 Jun 2020 20:37:35: start model_add_line... INFO @ Sun, 21 Jun 2020 20:37:35: start X-correlation... INFO @ Sun, 21 Jun 2020 20:37:35: end of X-cor INFO @ Sun, 21 Jun 2020 20:37:35: #2 finished! INFO @ Sun, 21 Jun 2020 20:37:35: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 20:37:35: #2 alternative fragment length(s) may be 4,47 bps INFO @ Sun, 21 Jun 2020 20:37:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.10_model.r WARNING @ Sun, 21 Jun 2020 20:37:35: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:37:35: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Sun, 21 Jun 2020 20:37:35: #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 20:37:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:37:35: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:37:41: 7000000 INFO @ Sun, 21 Jun 2020 20:37:48: 8000000 INFO @ Sun, 21 Jun 2020 20:37:55: 9000000 INFO @ Sun, 21 Jun 2020 20:37:57: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:38:02: 10000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:38:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:38:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:38:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.10_summits.bed INFO @ Sun, 21 Jun 2020 20:38:08: Done! pass1 - making usageList (604 chroms): 1 millis pass2 - checking and writing primary data (2093 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:38:09: 11000000 INFO @ Sun, 21 Jun 2020 20:38:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:38:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:38:12: #1 total tags in treatment: 11449479 INFO @ Sun, 21 Jun 2020 20:38:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:38:12: #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 20:38:13: #1 tags after filtering in treatment: 11449476 INFO @ Sun, 21 Jun 2020 20:38:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:38:13: #1 finished! INFO @ Sun, 21 Jun 2020 20:38:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:38:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:38:13: #2 number of paired peaks: 789 WARNING @ Sun, 21 Jun 2020 20:38:13: Fewer paired peaks (789) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 789 pairs to build model! INFO @ Sun, 21 Jun 2020 20:38:13: start model_add_line... INFO @ Sun, 21 Jun 2020 20:38:14: start X-correlation... INFO @ Sun, 21 Jun 2020 20:38:14: end of X-cor INFO @ Sun, 21 Jun 2020 20:38:14: #2 finished! INFO @ Sun, 21 Jun 2020 20:38:14: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 20:38:14: #2 alternative fragment length(s) may be 4,47 bps INFO @ Sun, 21 Jun 2020 20:38:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.20_model.r WARNING @ Sun, 21 Jun 2020 20:38:14: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:38:14: #2 You may need to consider one of the other alternative d(s): 4,47 WARNING @ Sun, 21 Jun 2020 20:38:14: #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 20:38:14: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:38:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:38:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:38:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:38:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:38:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4053366/SRX4053366.20_summits.bed INFO @ Sun, 21 Jun 2020 20:38:46: Done! pass1 - making usageList (394 chroms): 1 millis pass2 - checking and writing primary data (951 records, 4 fields): 11 millis CompletedMACS2peakCalling