Job ID = 6527822 SRX = SRX287758 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:26:49 prefetch.2.10.7: 1) Downloading 'SRR869947'... 2020-06-29T13:26:49 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:30:04 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:30:04 prefetch.2.10.7: 1) 'SRR869947' was downloaded successfully Read 26274958 spots for SRR869947/SRR869947.sra Written 26274958 spots for SRR869947/SRR869947.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: 00:09:58 26274958 reads; of these: 26274958 (100.00%) were unpaired; of these: 1296628 (4.93%) aligned 0 times 16585847 (63.12%) aligned exactly 1 time 8392483 (31.94%) aligned >1 times 95.07% overall alignment rate Time searching: 00:09:58 Overall time: 00:09:58 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4733813 / 24978330 = 0.1895 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 @ Mon, 29 Jun 2020 22:54:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.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 @ Mon, 29 Jun 2020 22:54:09: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:54:09: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:54:16: 1000000 INFO @ Mon, 29 Jun 2020 22:54:23: 2000000 INFO @ Mon, 29 Jun 2020 22:54:30: 3000000 INFO @ Mon, 29 Jun 2020 22:54:36: 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 @ Mon, 29 Jun 2020 22:54:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.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 @ Mon, 29 Jun 2020 22:54:39: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:54:39: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:54:44: 5000000 INFO @ Mon, 29 Jun 2020 22:54:47: 1000000 INFO @ Mon, 29 Jun 2020 22:54:51: 6000000 INFO @ Mon, 29 Jun 2020 22:54:54: 2000000 INFO @ Mon, 29 Jun 2020 22:54:59: 7000000 INFO @ Mon, 29 Jun 2020 22:55:02: 3000000 INFO @ Mon, 29 Jun 2020 22:55:07: 8000000 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 @ Mon, 29 Jun 2020 22:55:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.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 @ Mon, 29 Jun 2020 22:55:09: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:55:09: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:55:09: 4000000 INFO @ Mon, 29 Jun 2020 22:55:15: 9000000 INFO @ Mon, 29 Jun 2020 22:55:17: 5000000 INFO @ Mon, 29 Jun 2020 22:55:17: 1000000 INFO @ Mon, 29 Jun 2020 22:55:23: 10000000 INFO @ Mon, 29 Jun 2020 22:55:25: 6000000 INFO @ Mon, 29 Jun 2020 22:55:25: 2000000 INFO @ Mon, 29 Jun 2020 22:55:30: 11000000 INFO @ Mon, 29 Jun 2020 22:55:32: 7000000 INFO @ Mon, 29 Jun 2020 22:55:33: 3000000 INFO @ Mon, 29 Jun 2020 22:55:38: 12000000 INFO @ Mon, 29 Jun 2020 22:55:40: 8000000 INFO @ Mon, 29 Jun 2020 22:55:40: 4000000 INFO @ Mon, 29 Jun 2020 22:55:46: 13000000 INFO @ Mon, 29 Jun 2020 22:55:48: 9000000 INFO @ Mon, 29 Jun 2020 22:55:48: 5000000 INFO @ Mon, 29 Jun 2020 22:55:54: 14000000 INFO @ Mon, 29 Jun 2020 22:55:56: 10000000 INFO @ Mon, 29 Jun 2020 22:55:56: 6000000 INFO @ Mon, 29 Jun 2020 22:56:02: 15000000 INFO @ Mon, 29 Jun 2020 22:56:03: 11000000 INFO @ Mon, 29 Jun 2020 22:56:04: 7000000 INFO @ Mon, 29 Jun 2020 22:56:10: 16000000 INFO @ Mon, 29 Jun 2020 22:56:10: 12000000 INFO @ Mon, 29 Jun 2020 22:56:11: 8000000 INFO @ Mon, 29 Jun 2020 22:56:18: 17000000 INFO @ Mon, 29 Jun 2020 22:56:18: 13000000 INFO @ Mon, 29 Jun 2020 22:56:19: 9000000 INFO @ Mon, 29 Jun 2020 22:56:26: 18000000 INFO @ Mon, 29 Jun 2020 22:56:26: 14000000 INFO @ Mon, 29 Jun 2020 22:56:27: 10000000 INFO @ Mon, 29 Jun 2020 22:56:34: 19000000 INFO @ Mon, 29 Jun 2020 22:56:34: 15000000 INFO @ Mon, 29 Jun 2020 22:56:35: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:56:41: 20000000 INFO @ Mon, 29 Jun 2020 22:56:42: 16000000 INFO @ Mon, 29 Jun 2020 22:56:42: 12000000 INFO @ Mon, 29 Jun 2020 22:56:43: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:56:43: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:56:43: #1 total tags in treatment: 20244517 INFO @ Mon, 29 Jun 2020 22:56:43: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:56:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:56:44: #1 tags after filtering in treatment: 20244517 INFO @ Mon, 29 Jun 2020 22:56:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:56:44: #1 finished! INFO @ Mon, 29 Jun 2020 22:56:44: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:56:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:56:45: #2 number of paired peaks: 180 WARNING @ Mon, 29 Jun 2020 22:56:45: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Mon, 29 Jun 2020 22:56:45: start model_add_line... INFO @ Mon, 29 Jun 2020 22:56:45: start X-correlation... INFO @ Mon, 29 Jun 2020 22:56:45: end of X-cor INFO @ Mon, 29 Jun 2020 22:56:45: #2 finished! INFO @ Mon, 29 Jun 2020 22:56:45: #2 predicted fragment length is 46 bps INFO @ Mon, 29 Jun 2020 22:56:45: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 29 Jun 2020 22:56:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.05_model.r WARNING @ Mon, 29 Jun 2020 22:56:45: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:56:45: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 29 Jun 2020 22:56:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:56:45: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:56:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:56:50: 13000000 INFO @ Mon, 29 Jun 2020 22:56:50: 17000000 INFO @ Mon, 29 Jun 2020 22:56:57: 14000000 INFO @ Mon, 29 Jun 2020 22:56:58: 18000000 INFO @ Mon, 29 Jun 2020 22:57:05: 15000000 INFO @ Mon, 29 Jun 2020 22:57:05: 19000000 INFO @ Mon, 29 Jun 2020 22:57:12: 16000000 INFO @ Mon, 29 Jun 2020 22:57:13: 20000000 INFO @ Mon, 29 Jun 2020 22:57:15: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:57:15: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:57:15: #1 total tags in treatment: 20244517 INFO @ Mon, 29 Jun 2020 22:57:15: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:57:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:57:15: #1 tags after filtering in treatment: 20244517 INFO @ Mon, 29 Jun 2020 22:57:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:57:15: #1 finished! INFO @ Mon, 29 Jun 2020 22:57:15: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:57:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:57:16: #2 number of paired peaks: 180 WARNING @ Mon, 29 Jun 2020 22:57:16: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Mon, 29 Jun 2020 22:57:16: start model_add_line... INFO @ Mon, 29 Jun 2020 22:57:16: start X-correlation... INFO @ Mon, 29 Jun 2020 22:57:16: end of X-cor INFO @ Mon, 29 Jun 2020 22:57:16: #2 finished! INFO @ Mon, 29 Jun 2020 22:57:16: #2 predicted fragment length is 46 bps INFO @ Mon, 29 Jun 2020 22:57:16: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 29 Jun 2020 22:57:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.10_model.r WARNING @ Mon, 29 Jun 2020 22:57:16: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:57:16: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 29 Jun 2020 22:57:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:57:16: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:57:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:57:19: 17000000 INFO @ Mon, 29 Jun 2020 22:57:23: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:57:26: 18000000 INFO @ Mon, 29 Jun 2020 22:57:33: 19000000 INFO @ Mon, 29 Jun 2020 22:57:40: 20000000 INFO @ Mon, 29 Jun 2020 22:57:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:57:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:57:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.05_summits.bed INFO @ Mon, 29 Jun 2020 22:57:41: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2302 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:57:42: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:57:42: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:57:42: #1 total tags in treatment: 20244517 INFO @ Mon, 29 Jun 2020 22:57:42: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:57:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:57:42: #1 tags after filtering in treatment: 20244517 INFO @ Mon, 29 Jun 2020 22:57:42: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:57:42: #1 finished! INFO @ Mon, 29 Jun 2020 22:57:42: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:57:42: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:57:43: #2 number of paired peaks: 180 WARNING @ Mon, 29 Jun 2020 22:57:43: Fewer paired peaks (180) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 180 pairs to build model! INFO @ Mon, 29 Jun 2020 22:57:43: start model_add_line... INFO @ Mon, 29 Jun 2020 22:57:43: start X-correlation... INFO @ Mon, 29 Jun 2020 22:57:43: end of X-cor INFO @ Mon, 29 Jun 2020 22:57:43: #2 finished! INFO @ Mon, 29 Jun 2020 22:57:43: #2 predicted fragment length is 46 bps INFO @ Mon, 29 Jun 2020 22:57:43: #2 alternative fragment length(s) may be 46 bps INFO @ Mon, 29 Jun 2020 22:57:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.20_model.r WARNING @ Mon, 29 Jun 2020 22:57:43: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:57:43: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Mon, 29 Jun 2020 22:57:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:57:43: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:57:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:57:52: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:58:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:58:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:58:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.10_summits.bed INFO @ Mon, 29 Jun 2020 22:58:10: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1873 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:58:21: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:58:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:58:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:58:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287758/SRX287758.20_summits.bed INFO @ Mon, 29 Jun 2020 22:58:40: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1443 records, 4 fields): 3 millis CompletedMACS2peakCalling