Job ID = 6456531 SRX = SRX3630330 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:55:16 prefetch.2.10.7: 1) Downloading 'SRR6652852'... 2020-06-21T10:55:16 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:59:46 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:59:46 prefetch.2.10.7: 1) 'SRR6652852' was downloaded successfully 2020-06-21T10:59:46 prefetch.2.10.7: 'SRR6652852' has 0 unresolved dependencies Read 31067185 spots for SRR6652852/SRR6652852.sra Written 31067185 spots for SRR6652852/SRR6652852.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: 00:13:52 31067185 reads; of these: 31067185 (100.00%) were unpaired; of these: 1072861 (3.45%) aligned 0 times 10571304 (34.03%) aligned exactly 1 time 19423020 (62.52%) aligned >1 times 96.55% overall alignment rate Time searching: 00:13:52 Overall time: 00:13:52 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] 11598960 / 29994324 = 0.3867 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 20:24:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.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 20:24:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:24:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:24:10: 1000000 INFO @ Sun, 21 Jun 2020 20:24:16: 2000000 INFO @ Sun, 21 Jun 2020 20:24:22: 3000000 INFO @ Sun, 21 Jun 2020 20:24:28: 4000000 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 20:24:34: 5000000 INFO @ Sun, 21 Jun 2020 20:24:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.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 20:24:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:24:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:24:40: 6000000 INFO @ Sun, 21 Jun 2020 20:24:41: 1000000 INFO @ Sun, 21 Jun 2020 20:24:46: 7000000 INFO @ Sun, 21 Jun 2020 20:24:48: 2000000 INFO @ Sun, 21 Jun 2020 20:24:52: 8000000 INFO @ Sun, 21 Jun 2020 20:24:55: 3000000 INFO @ Sun, 21 Jun 2020 20:24:58: 9000000 INFO @ Sun, 21 Jun 2020 20:25:01: 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 20:25:04: 10000000 INFO @ Sun, 21 Jun 2020 20:25:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.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 20:25:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:25:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:25:08: 5000000 INFO @ Sun, 21 Jun 2020 20:25:09: 11000000 INFO @ Sun, 21 Jun 2020 20:25:11: 1000000 INFO @ Sun, 21 Jun 2020 20:25:15: 12000000 INFO @ Sun, 21 Jun 2020 20:25:15: 6000000 INFO @ Sun, 21 Jun 2020 20:25:18: 2000000 INFO @ Sun, 21 Jun 2020 20:25:20: 13000000 INFO @ Sun, 21 Jun 2020 20:25:22: 7000000 INFO @ Sun, 21 Jun 2020 20:25:25: 3000000 INFO @ Sun, 21 Jun 2020 20:25:26: 14000000 INFO @ Sun, 21 Jun 2020 20:25:29: 8000000 INFO @ Sun, 21 Jun 2020 20:25:32: 15000000 INFO @ Sun, 21 Jun 2020 20:25:32: 4000000 INFO @ Sun, 21 Jun 2020 20:25:35: 9000000 INFO @ Sun, 21 Jun 2020 20:25:37: 16000000 INFO @ Sun, 21 Jun 2020 20:25:39: 5000000 INFO @ Sun, 21 Jun 2020 20:25:42: 10000000 INFO @ Sun, 21 Jun 2020 20:25:43: 17000000 INFO @ Sun, 21 Jun 2020 20:25:46: 6000000 INFO @ Sun, 21 Jun 2020 20:25:48: 18000000 INFO @ Sun, 21 Jun 2020 20:25:49: 11000000 INFO @ Sun, 21 Jun 2020 20:25:51: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:25:51: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:25:51: #1 total tags in treatment: 18395364 INFO @ Sun, 21 Jun 2020 20:25:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:25:51: #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 20:25:52: #1 tags after filtering in treatment: 18395342 INFO @ Sun, 21 Jun 2020 20:25:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:25:52: #1 finished! INFO @ Sun, 21 Jun 2020 20:25:52: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:25:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:25:52: 7000000 INFO @ Sun, 21 Jun 2020 20:25:53: #2 number of paired peaks: 3917 INFO @ Sun, 21 Jun 2020 20:25:53: start model_add_line... INFO @ Sun, 21 Jun 2020 20:25:54: start X-correlation... INFO @ Sun, 21 Jun 2020 20:25:54: end of X-cor INFO @ Sun, 21 Jun 2020 20:25:54: #2 finished! INFO @ Sun, 21 Jun 2020 20:25:54: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 20:25:54: #2 alternative fragment length(s) may be 2,56 bps INFO @ Sun, 21 Jun 2020 20:25:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.05_model.r WARNING @ Sun, 21 Jun 2020 20:25:54: #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 20:25:54: #2 You may need to consider one of the other alternative d(s): 2,56 WARNING @ Sun, 21 Jun 2020 20:25:54: #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 20:25:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:25:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:25:55: 12000000 INFO @ Sun, 21 Jun 2020 20:25:59: 8000000 INFO @ Sun, 21 Jun 2020 20:26:01: 13000000 INFO @ Sun, 21 Jun 2020 20:26:05: 9000000 INFO @ Sun, 21 Jun 2020 20:26:08: 14000000 INFO @ Sun, 21 Jun 2020 20:26:11: 10000000 INFO @ Sun, 21 Jun 2020 20:26:15: 15000000 INFO @ Sun, 21 Jun 2020 20:26:17: 11000000 INFO @ Sun, 21 Jun 2020 20:26:21: 16000000 INFO @ Sun, 21 Jun 2020 20:26:23: 12000000 INFO @ Sun, 21 Jun 2020 20:26:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:26:27: 17000000 INFO @ Sun, 21 Jun 2020 20:26:29: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:26:34: 18000000 INFO @ Sun, 21 Jun 2020 20:26:36: 14000000 INFO @ Sun, 21 Jun 2020 20:26:36: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:26:36: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:26:36: #1 total tags in treatment: 18395364 INFO @ Sun, 21 Jun 2020 20:26:36: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:26:36: #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 20:26:38: #1 tags after filtering in treatment: 18395342 INFO @ Sun, 21 Jun 2020 20:26:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:26:38: #1 finished! INFO @ Sun, 21 Jun 2020 20:26:38: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:26:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:26:39: #2 number of paired peaks: 3917 INFO @ Sun, 21 Jun 2020 20:26:39: start model_add_line... INFO @ Sun, 21 Jun 2020 20:26:40: start X-correlation... INFO @ Sun, 21 Jun 2020 20:26:40: end of X-cor INFO @ Sun, 21 Jun 2020 20:26:40: #2 finished! INFO @ Sun, 21 Jun 2020 20:26:40: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 20:26:40: #2 alternative fragment length(s) may be 2,56 bps INFO @ Sun, 21 Jun 2020 20:26:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.10_model.r WARNING @ Sun, 21 Jun 2020 20:26:40: #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 20:26:40: #2 You may need to consider one of the other alternative d(s): 2,56 WARNING @ Sun, 21 Jun 2020 20:26:40: #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 20:26:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:26:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:26:42: 15000000 INFO @ Sun, 21 Jun 2020 20:26:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:26:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:26:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.05_summits.bed INFO @ Sun, 21 Jun 2020 20:26:43: Done! pass1 - making usageList (1136 chroms): 3 millis pass2 - checking and writing primary data (7374 records, 4 fields): 69 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:26:47: 16000000 INFO @ Sun, 21 Jun 2020 20:26:53: 17000000 INFO @ Sun, 21 Jun 2020 20:26:59: 18000000 INFO @ Sun, 21 Jun 2020 20:27:02: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:27:02: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:27:02: #1 total tags in treatment: 18395364 INFO @ Sun, 21 Jun 2020 20:27:02: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:27:02: #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 20:27:02: #1 tags after filtering in treatment: 18395342 INFO @ Sun, 21 Jun 2020 20:27:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:27:02: #1 finished! INFO @ Sun, 21 Jun 2020 20:27:02: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:27:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:27:04: #2 number of paired peaks: 3917 INFO @ Sun, 21 Jun 2020 20:27:04: start model_add_line... INFO @ Sun, 21 Jun 2020 20:27:04: start X-correlation... INFO @ Sun, 21 Jun 2020 20:27:04: end of X-cor INFO @ Sun, 21 Jun 2020 20:27:04: #2 finished! INFO @ Sun, 21 Jun 2020 20:27:04: #2 predicted fragment length is 56 bps INFO @ Sun, 21 Jun 2020 20:27:04: #2 alternative fragment length(s) may be 2,56 bps INFO @ Sun, 21 Jun 2020 20:27:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.20_model.r WARNING @ Sun, 21 Jun 2020 20:27:04: #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 20:27:04: #2 You may need to consider one of the other alternative d(s): 2,56 WARNING @ Sun, 21 Jun 2020 20:27:04: #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 20:27:04: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:27:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:27:14: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:27:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:27:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:27:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.10_summits.bed INFO @ Sun, 21 Jun 2020 20:27:31: Done! pass1 - making usageList (960 chroms): 2 millis pass2 - checking and writing primary data (3722 records, 4 fields): 56 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:27:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:27:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:27:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:27:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX3630330/SRX3630330.20_summits.bed INFO @ Sun, 21 Jun 2020 20:27:55: Done! pass1 - making usageList (722 chroms): 2 millis pass2 - checking and writing primary data (2417 records, 4 fields): 41 millis CompletedMACS2peakCalling