Job ID = 6457834 SRX = SRX4801799 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:59:03 prefetch.2.10.7: 1) Downloading 'SRR7968384'... 2020-06-21T11:59:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:04:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:04:22 prefetch.2.10.7: 1) 'SRR7968384' was downloaded successfully Read 33068527 spots for SRR7968384/SRR7968384.sra Written 33068527 spots for SRR7968384/SRR7968384.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: 00:12:28 33068527 reads; of these: 33068527 (100.00%) were unpaired; of these: 1038337 (3.14%) aligned 0 times 22354158 (67.60%) aligned exactly 1 time 9676032 (29.26%) aligned >1 times 96.86% overall alignment rate Time searching: 00:12:28 Overall time: 00:12:28 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 16 files... [bam_rmdupse_core] 5143225 / 32030190 = 0.1606 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 21:26:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.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 21:26:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:26:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:26:57: 1000000 INFO @ Sun, 21 Jun 2020 21:27:03: 2000000 INFO @ Sun, 21 Jun 2020 21:27:08: 3000000 INFO @ Sun, 21 Jun 2020 21:27:14: 4000000 INFO @ Sun, 21 Jun 2020 21:27:19: 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 21:27:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.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 21:27:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:27:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:27:25: 6000000 INFO @ Sun, 21 Jun 2020 21:27:28: 1000000 INFO @ Sun, 21 Jun 2020 21:27:30: 7000000 INFO @ Sun, 21 Jun 2020 21:27:33: 2000000 INFO @ Sun, 21 Jun 2020 21:27:36: 8000000 INFO @ Sun, 21 Jun 2020 21:27:39: 3000000 INFO @ Sun, 21 Jun 2020 21:27:42: 9000000 INFO @ Sun, 21 Jun 2020 21:27:45: 4000000 INFO @ Sun, 21 Jun 2020 21:27:48: 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 21:27:51: 5000000 INFO @ Sun, 21 Jun 2020 21:27:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.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 21:27:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:27:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:27:54: 11000000 INFO @ Sun, 21 Jun 2020 21:27:57: 6000000 INFO @ Sun, 21 Jun 2020 21:27:58: 1000000 INFO @ Sun, 21 Jun 2020 21:28:00: 12000000 INFO @ Sun, 21 Jun 2020 21:28:03: 7000000 INFO @ Sun, 21 Jun 2020 21:28:04: 2000000 INFO @ Sun, 21 Jun 2020 21:28:06: 13000000 INFO @ Sun, 21 Jun 2020 21:28:09: 8000000 INFO @ Sun, 21 Jun 2020 21:28:11: 3000000 INFO @ Sun, 21 Jun 2020 21:28:13: 14000000 INFO @ Sun, 21 Jun 2020 21:28:15: 9000000 INFO @ Sun, 21 Jun 2020 21:28:17: 4000000 INFO @ Sun, 21 Jun 2020 21:28:19: 15000000 INFO @ Sun, 21 Jun 2020 21:28:22: 10000000 INFO @ Sun, 21 Jun 2020 21:28:23: 5000000 INFO @ Sun, 21 Jun 2020 21:28:25: 16000000 INFO @ Sun, 21 Jun 2020 21:28:28: 11000000 INFO @ Sun, 21 Jun 2020 21:28:29: 6000000 INFO @ Sun, 21 Jun 2020 21:28:31: 17000000 INFO @ Sun, 21 Jun 2020 21:28:34: 12000000 INFO @ Sun, 21 Jun 2020 21:28:36: 7000000 INFO @ Sun, 21 Jun 2020 21:28:38: 18000000 INFO @ Sun, 21 Jun 2020 21:28:40: 13000000 INFO @ Sun, 21 Jun 2020 21:28:42: 8000000 INFO @ Sun, 21 Jun 2020 21:28:44: 19000000 INFO @ Sun, 21 Jun 2020 21:28:47: 14000000 INFO @ Sun, 21 Jun 2020 21:28:48: 9000000 INFO @ Sun, 21 Jun 2020 21:28:51: 20000000 INFO @ Sun, 21 Jun 2020 21:28:53: 15000000 INFO @ Sun, 21 Jun 2020 21:28:54: 10000000 INFO @ Sun, 21 Jun 2020 21:28:58: 21000000 INFO @ Sun, 21 Jun 2020 21:29:00: 16000000 INFO @ Sun, 21 Jun 2020 21:29:01: 11000000 INFO @ Sun, 21 Jun 2020 21:29:05: 22000000 INFO @ Sun, 21 Jun 2020 21:29:06: 17000000 INFO @ Sun, 21 Jun 2020 21:29:08: 12000000 INFO @ Sun, 21 Jun 2020 21:29:12: 23000000 INFO @ Sun, 21 Jun 2020 21:29:12: 18000000 INFO @ Sun, 21 Jun 2020 21:29:14: 13000000 INFO @ Sun, 21 Jun 2020 21:29:18: 24000000 INFO @ Sun, 21 Jun 2020 21:29:19: 19000000 INFO @ Sun, 21 Jun 2020 21:29:20: 14000000 INFO @ Sun, 21 Jun 2020 21:29:24: 25000000 INFO @ Sun, 21 Jun 2020 21:29:25: 20000000 INFO @ Sun, 21 Jun 2020 21:29:27: 15000000 INFO @ Sun, 21 Jun 2020 21:29:30: 26000000 INFO @ Sun, 21 Jun 2020 21:29:32: 21000000 INFO @ Sun, 21 Jun 2020 21:29:34: 16000000 INFO @ Sun, 21 Jun 2020 21:29:36: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:29:36: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:29:36: #1 total tags in treatment: 26886965 INFO @ Sun, 21 Jun 2020 21:29:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:29:36: #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 21:29:37: #1 tags after filtering in treatment: 26886904 INFO @ Sun, 21 Jun 2020 21:29:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:29:37: #1 finished! INFO @ Sun, 21 Jun 2020 21:29:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:29:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:29:39: #2 number of paired peaks: 680 WARNING @ Sun, 21 Jun 2020 21:29:39: Fewer paired peaks (680) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 680 pairs to build model! INFO @ Sun, 21 Jun 2020 21:29:39: start model_add_line... INFO @ Sun, 21 Jun 2020 21:29:39: 22000000 INFO @ Sun, 21 Jun 2020 21:29:39: start X-correlation... INFO @ Sun, 21 Jun 2020 21:29:39: end of X-cor INFO @ Sun, 21 Jun 2020 21:29:39: #2 finished! INFO @ Sun, 21 Jun 2020 21:29:39: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 21:29:39: #2 alternative fragment length(s) may be 1,62,570,586 bps INFO @ Sun, 21 Jun 2020 21:29:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.05_model.r WARNING @ Sun, 21 Jun 2020 21:29:39: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:29:39: #2 You may need to consider one of the other alternative d(s): 1,62,570,586 WARNING @ Sun, 21 Jun 2020 21:29:39: #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 21:29:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:29:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:29:40: 17000000 INFO @ Sun, 21 Jun 2020 21:29:46: 23000000 INFO @ Sun, 21 Jun 2020 21:29:47: 18000000 INFO @ Sun, 21 Jun 2020 21:29:52: 24000000 INFO @ Sun, 21 Jun 2020 21:29:54: 19000000 INFO @ Sun, 21 Jun 2020 21:29:59: 25000000 INFO @ Sun, 21 Jun 2020 21:30:00: 20000000 INFO @ Sun, 21 Jun 2020 21:30:06: 26000000 INFO @ Sun, 21 Jun 2020 21:30:07: 21000000 INFO @ Sun, 21 Jun 2020 21:30:12: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:30:12: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:30:12: #1 total tags in treatment: 26886965 INFO @ Sun, 21 Jun 2020 21:30:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:30:12: #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 21:30:13: #1 tags after filtering in treatment: 26886904 INFO @ Sun, 21 Jun 2020 21:30:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:30:13: #1 finished! INFO @ Sun, 21 Jun 2020 21:30:13: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:30:13: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:30:14: 22000000 INFO @ Sun, 21 Jun 2020 21:30:15: #2 number of paired peaks: 680 WARNING @ Sun, 21 Jun 2020 21:30:15: Fewer paired peaks (680) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 680 pairs to build model! INFO @ Sun, 21 Jun 2020 21:30:15: start model_add_line... INFO @ Sun, 21 Jun 2020 21:30:15: start X-correlation... INFO @ Sun, 21 Jun 2020 21:30:15: end of X-cor INFO @ Sun, 21 Jun 2020 21:30:15: #2 finished! INFO @ Sun, 21 Jun 2020 21:30:15: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 21:30:15: #2 alternative fragment length(s) may be 1,62,570,586 bps INFO @ Sun, 21 Jun 2020 21:30:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.10_model.r WARNING @ Sun, 21 Jun 2020 21:30:15: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:30:15: #2 You may need to consider one of the other alternative d(s): 1,62,570,586 WARNING @ Sun, 21 Jun 2020 21:30:15: #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 21:30:15: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:30:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:30:20: 23000000 INFO @ Sun, 21 Jun 2020 21:30:26: 24000000 INFO @ Sun, 21 Jun 2020 21:30:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:30:32: 25000000 INFO @ Sun, 21 Jun 2020 21:30:38: 26000000 INFO @ Sun, 21 Jun 2020 21:30:43: #1 tag size is determined as 68 bps INFO @ Sun, 21 Jun 2020 21:30:43: #1 tag size = 68 INFO @ Sun, 21 Jun 2020 21:30:43: #1 total tags in treatment: 26886965 INFO @ Sun, 21 Jun 2020 21:30:43: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:30:43: #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 21:30:44: #1 tags after filtering in treatment: 26886904 INFO @ Sun, 21 Jun 2020 21:30:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:30:44: #1 finished! INFO @ Sun, 21 Jun 2020 21:30:44: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:30:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:30:46: #2 number of paired peaks: 680 WARNING @ Sun, 21 Jun 2020 21:30:46: Fewer paired peaks (680) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 680 pairs to build model! INFO @ Sun, 21 Jun 2020 21:30:46: start model_add_line... INFO @ Sun, 21 Jun 2020 21:30:46: start X-correlation... INFO @ Sun, 21 Jun 2020 21:30:46: end of X-cor INFO @ Sun, 21 Jun 2020 21:30:46: #2 finished! INFO @ Sun, 21 Jun 2020 21:30:46: #2 predicted fragment length is 62 bps INFO @ Sun, 21 Jun 2020 21:30:46: #2 alternative fragment length(s) may be 1,62,570,586 bps INFO @ Sun, 21 Jun 2020 21:30:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.20_model.r WARNING @ Sun, 21 Jun 2020 21:30:46: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:30:46: #2 You may need to consider one of the other alternative d(s): 1,62,570,586 WARNING @ Sun, 21 Jun 2020 21:30:46: #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 21:30:46: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:30:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:30:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:30:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:30:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.05_summits.bed INFO @ Sun, 21 Jun 2020 21:30:53: Done! pass1 - making usageList (710 chroms): 1 millis pass2 - checking and writing primary data (3826 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:31:03: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:31:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:31:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:31:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.10_summits.bed INFO @ Sun, 21 Jun 2020 21:31:27: Done! pass1 - making usageList (572 chroms): 2 millis pass2 - checking and writing primary data (2105 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:31:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:31:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:31:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:31:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4801799/SRX4801799.20_summits.bed INFO @ Sun, 21 Jun 2020 21:31:58: Done! pass1 - making usageList (340 chroms): 1 millis pass2 - checking and writing primary data (801 records, 4 fields): 11 millis CompletedMACS2peakCalling