Job ID = 6453709 SRX = SRX1433355 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:38:24 prefetch.2.10.7: 1) Downloading 'SRR2919820'... 2020-06-21T08:38:24 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:42:40 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:42:40 prefetch.2.10.7: 1) 'SRR2919820' was downloaded successfully Read 39459749 spots for SRR2919820/SRR2919820.sra Written 39459749 spots for SRR2919820/SRR2919820.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: 00:18:31 39459749 reads; of these: 39459749 (100.00%) were unpaired; of these: 2002439 (5.07%) aligned 0 times 17445722 (44.21%) aligned exactly 1 time 20011588 (50.71%) aligned >1 times 94.93% overall alignment rate Time searching: 00:18:31 Overall time: 00:18:31 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] 20568101 / 37457310 = 0.5491 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 18:10:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.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 18:10:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:10:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:10:17: 1000000 INFO @ Sun, 21 Jun 2020 18:10:23: 2000000 INFO @ Sun, 21 Jun 2020 18:10:28: 3000000 INFO @ Sun, 21 Jun 2020 18:10:34: 4000000 INFO @ Sun, 21 Jun 2020 18:10:39: 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 18:10:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.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 18:10:42: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:10:42: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:10:45: 6000000 INFO @ Sun, 21 Jun 2020 18:10:48: 1000000 INFO @ Sun, 21 Jun 2020 18:10:52: 7000000 INFO @ Sun, 21 Jun 2020 18:10:54: 2000000 INFO @ Sun, 21 Jun 2020 18:10:58: 8000000 INFO @ Sun, 21 Jun 2020 18:11:01: 3000000 INFO @ Sun, 21 Jun 2020 18:11:04: 9000000 INFO @ Sun, 21 Jun 2020 18:11:07: 4000000 INFO @ Sun, 21 Jun 2020 18:11:10: 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 18:11:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.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 18:11:12: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:11:12: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:11:13: 5000000 INFO @ Sun, 21 Jun 2020 18:11:17: 11000000 INFO @ Sun, 21 Jun 2020 18:11:19: 1000000 INFO @ Sun, 21 Jun 2020 18:11:20: 6000000 INFO @ Sun, 21 Jun 2020 18:11:23: 12000000 INFO @ Sun, 21 Jun 2020 18:11:27: 7000000 INFO @ Sun, 21 Jun 2020 18:11:27: 2000000 INFO @ Sun, 21 Jun 2020 18:11:30: 13000000 INFO @ Sun, 21 Jun 2020 18:11:33: 8000000 INFO @ Sun, 21 Jun 2020 18:11:34: 3000000 INFO @ Sun, 21 Jun 2020 18:11:37: 14000000 INFO @ Sun, 21 Jun 2020 18:11:40: 9000000 INFO @ Sun, 21 Jun 2020 18:11:42: 4000000 INFO @ Sun, 21 Jun 2020 18:11:44: 15000000 INFO @ Sun, 21 Jun 2020 18:11:47: 10000000 INFO @ Sun, 21 Jun 2020 18:11:49: 5000000 INFO @ Sun, 21 Jun 2020 18:11:51: 16000000 INFO @ Sun, 21 Jun 2020 18:11:53: 11000000 INFO @ Sun, 21 Jun 2020 18:11:57: 6000000 INFO @ Sun, 21 Jun 2020 18:11:57: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:11:57: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:11:57: #1 total tags in treatment: 16889209 INFO @ Sun, 21 Jun 2020 18:11:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:11:57: #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 18:11:58: #1 tags after filtering in treatment: 16889140 INFO @ Sun, 21 Jun 2020 18:11:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:11:58: #1 finished! INFO @ Sun, 21 Jun 2020 18:11:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:11:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:11:59: #2 number of paired peaks: 2985 INFO @ Sun, 21 Jun 2020 18:11:59: start model_add_line... INFO @ Sun, 21 Jun 2020 18:11:59: start X-correlation... INFO @ Sun, 21 Jun 2020 18:11:59: end of X-cor INFO @ Sun, 21 Jun 2020 18:11:59: #2 finished! INFO @ Sun, 21 Jun 2020 18:11:59: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 18:11:59: #2 alternative fragment length(s) may be 1,56 bps INFO @ Sun, 21 Jun 2020 18:11:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.05_model.r WARNING @ Sun, 21 Jun 2020 18:11:59: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:11:59: #2 You may need to consider one of the other alternative d(s): 1,56 WARNING @ Sun, 21 Jun 2020 18:11:59: #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 18:11:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:11:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:12:00: 12000000 INFO @ Sun, 21 Jun 2020 18:12:04: 7000000 INFO @ Sun, 21 Jun 2020 18:12:07: 13000000 INFO @ Sun, 21 Jun 2020 18:12:12: 8000000 INFO @ Sun, 21 Jun 2020 18:12:14: 14000000 INFO @ Sun, 21 Jun 2020 18:12:19: 9000000 INFO @ Sun, 21 Jun 2020 18:12:21: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:12:26: 10000000 INFO @ Sun, 21 Jun 2020 18:12:27: 16000000 INFO @ Sun, 21 Jun 2020 18:12:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:12:34: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:12:34: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:12:34: #1 total tags in treatment: 16889209 INFO @ Sun, 21 Jun 2020 18:12:34: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:12:34: #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 18:12:34: 11000000 INFO @ Sun, 21 Jun 2020 18:12:34: #1 tags after filtering in treatment: 16889140 INFO @ Sun, 21 Jun 2020 18:12:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:12:34: #1 finished! INFO @ Sun, 21 Jun 2020 18:12:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:12:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:12:36: #2 number of paired peaks: 2985 INFO @ Sun, 21 Jun 2020 18:12:36: start model_add_line... INFO @ Sun, 21 Jun 2020 18:12:36: start X-correlation... INFO @ Sun, 21 Jun 2020 18:12:36: end of X-cor INFO @ Sun, 21 Jun 2020 18:12:36: #2 finished! INFO @ Sun, 21 Jun 2020 18:12:36: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 18:12:36: #2 alternative fragment length(s) may be 1,56 bps INFO @ Sun, 21 Jun 2020 18:12:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.10_model.r WARNING @ Sun, 21 Jun 2020 18:12:36: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:12:36: #2 You may need to consider one of the other alternative d(s): 1,56 WARNING @ Sun, 21 Jun 2020 18:12:36: #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 18:12:36: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:12:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:12:41: 12000000 INFO @ Sun, 21 Jun 2020 18:12:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:12:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:12:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.05_summits.bed INFO @ Sun, 21 Jun 2020 18:12:47: Done! INFO @ Sun, 21 Jun 2020 18:12:48: 13000000 pass1 - making usageList (820 chroms): 2 millis pass2 - checking and writing primary data (5692 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:12:54: 14000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:13:01: 15000000 INFO @ Sun, 21 Jun 2020 18:13:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:13:08: 16000000 INFO @ Sun, 21 Jun 2020 18:13:14: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:13:14: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:13:14: #1 total tags in treatment: 16889209 INFO @ Sun, 21 Jun 2020 18:13:14: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:13:14: #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 18:13:15: #1 tags after filtering in treatment: 16889140 INFO @ Sun, 21 Jun 2020 18:13:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:13:15: #1 finished! INFO @ Sun, 21 Jun 2020 18:13:15: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:13:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:13:16: #2 number of paired peaks: 2985 INFO @ Sun, 21 Jun 2020 18:13:16: start model_add_line... INFO @ Sun, 21 Jun 2020 18:13:16: start X-correlation... INFO @ Sun, 21 Jun 2020 18:13:16: end of X-cor INFO @ Sun, 21 Jun 2020 18:13:16: #2 finished! INFO @ Sun, 21 Jun 2020 18:13:16: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 18:13:16: #2 alternative fragment length(s) may be 1,56 bps INFO @ Sun, 21 Jun 2020 18:13:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.20_model.r WARNING @ Sun, 21 Jun 2020 18:13:16: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:13:16: #2 You may need to consider one of the other alternative d(s): 1,56 WARNING @ Sun, 21 Jun 2020 18:13:16: #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 18:13:16: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:13:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:13:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:13:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:13:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.10_summits.bed INFO @ Sun, 21 Jun 2020 18:13:23: Done! pass1 - making usageList (677 chroms): 1 millis pass2 - checking and writing primary data (2782 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:13:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:14:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:14:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:14:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX1433355/SRX1433355.20_summits.bed INFO @ Sun, 21 Jun 2020 18:14:04: Done! pass1 - making usageList (548 chroms): 1 millis pass2 - checking and writing primary data (1873 records, 4 fields): 16 millis CompletedMACS2peakCalling