Job ID = 8069485 SRX = SRX7191474 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-08-08T03:33:29 prefetch.2.10.7: 1) Downloading 'SRR10502458'... 2020-08-08T03:33:29 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:34:58 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:34:59 prefetch.2.10.7: 'SRR10502458' is valid 2020-08-08T03:34:59 prefetch.2.10.7: 1) 'SRR10502458' was downloaded successfully Read 17112053 spots for SRR10502458/SRR10502458.sra Written 17112053 spots for SRR10502458/SRR10502458.sra fastq に変換しました。 bowtie でマッピング中... Your job 8069967 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:12 17112053 reads; of these: 17112053 (100.00%) were unpaired; of these: 819044 (4.79%) aligned 0 times 12463400 (72.83%) aligned exactly 1 time 3829609 (22.38%) aligned >1 times 95.21% overall alignment rate Time searching: 00:05:12 Overall time: 00:05:12 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 8 files... [bam_rmdupse_core] 1175980 / 16293009 = 0.0722 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 @ Sat, 08 Aug 2020 12:44:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.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 @ Sat, 08 Aug 2020 12:44:52: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:44:52: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:44:57: 1000000 INFO @ Sat, 08 Aug 2020 12:45:02: 2000000 INFO @ Sat, 08 Aug 2020 12:45:07: 3000000 INFO @ Sat, 08 Aug 2020 12:45:12: 4000000 INFO @ Sat, 08 Aug 2020 12:45:17: 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 @ Sat, 08 Aug 2020 12:45:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.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 @ Sat, 08 Aug 2020 12:45:22: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:45:22: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:45:22: 6000000 INFO @ Sat, 08 Aug 2020 12:45:27: 1000000 INFO @ Sat, 08 Aug 2020 12:45:27: 7000000 INFO @ Sat, 08 Aug 2020 12:45:33: 2000000 INFO @ Sat, 08 Aug 2020 12:45:33: 8000000 INFO @ Sat, 08 Aug 2020 12:45:38: 3000000 INFO @ Sat, 08 Aug 2020 12:45:38: 9000000 INFO @ Sat, 08 Aug 2020 12:45:44: 10000000 INFO @ Sat, 08 Aug 2020 12:45:44: 4000000 INFO @ Sat, 08 Aug 2020 12:45:49: 11000000 INFO @ Sat, 08 Aug 2020 12:45:49: 5000000 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 @ Sat, 08 Aug 2020 12:45:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.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 @ Sat, 08 Aug 2020 12:45:52: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:45:52: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:45:55: 6000000 INFO @ Sat, 08 Aug 2020 12:45:55: 12000000 INFO @ Sat, 08 Aug 2020 12:45:58: 1000000 INFO @ Sat, 08 Aug 2020 12:46:00: 7000000 INFO @ Sat, 08 Aug 2020 12:46:01: 13000000 INFO @ Sat, 08 Aug 2020 12:46:04: 2000000 INFO @ Sat, 08 Aug 2020 12:46:06: 8000000 INFO @ Sat, 08 Aug 2020 12:46:06: 14000000 INFO @ Sat, 08 Aug 2020 12:46:09: 3000000 INFO @ Sat, 08 Aug 2020 12:46:12: 9000000 INFO @ Sat, 08 Aug 2020 12:46:12: 15000000 INFO @ Sat, 08 Aug 2020 12:46:13: #1 tag size is determined as 50 bps INFO @ Sat, 08 Aug 2020 12:46:13: #1 tag size = 50 INFO @ Sat, 08 Aug 2020 12:46:13: #1 total tags in treatment: 15117029 INFO @ Sat, 08 Aug 2020 12:46:13: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:46:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:46:13: #1 tags after filtering in treatment: 15117029 INFO @ Sat, 08 Aug 2020 12:46:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Aug 2020 12:46:13: #1 finished! INFO @ Sat, 08 Aug 2020 12:46:13: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:46:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:46:14: #2 number of paired peaks: 464 WARNING @ Sat, 08 Aug 2020 12:46:14: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Sat, 08 Aug 2020 12:46:14: start model_add_line... INFO @ Sat, 08 Aug 2020 12:46:14: start X-correlation... INFO @ Sat, 08 Aug 2020 12:46:14: end of X-cor INFO @ Sat, 08 Aug 2020 12:46:14: #2 finished! INFO @ Sat, 08 Aug 2020 12:46:14: #2 predicted fragment length is 201 bps INFO @ Sat, 08 Aug 2020 12:46:14: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 08 Aug 2020 12:46:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.05_model.r INFO @ Sat, 08 Aug 2020 12:46:14: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:46:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:46:15: 4000000 INFO @ Sat, 08 Aug 2020 12:46:17: 10000000 INFO @ Sat, 08 Aug 2020 12:46:21: 5000000 INFO @ Sat, 08 Aug 2020 12:46:23: 11000000 INFO @ Sat, 08 Aug 2020 12:46:26: 6000000 INFO @ Sat, 08 Aug 2020 12:46:29: 12000000 INFO @ Sat, 08 Aug 2020 12:46:32: 7000000 INFO @ Sat, 08 Aug 2020 12:46:34: 13000000 INFO @ Sat, 08 Aug 2020 12:46:37: 8000000 INFO @ Sat, 08 Aug 2020 12:46:40: 14000000 INFO @ Sat, 08 Aug 2020 12:46:43: 9000000 INFO @ Sat, 08 Aug 2020 12:46:45: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:46:46: 15000000 INFO @ Sat, 08 Aug 2020 12:46:46: #1 tag size is determined as 50 bps INFO @ Sat, 08 Aug 2020 12:46:46: #1 tag size = 50 INFO @ Sat, 08 Aug 2020 12:46:46: #1 total tags in treatment: 15117029 INFO @ Sat, 08 Aug 2020 12:46:46: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:46:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:46:47: #1 tags after filtering in treatment: 15117029 INFO @ Sat, 08 Aug 2020 12:46:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Aug 2020 12:46:47: #1 finished! INFO @ Sat, 08 Aug 2020 12:46:47: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:46:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:46:48: #2 number of paired peaks: 464 WARNING @ Sat, 08 Aug 2020 12:46:48: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Sat, 08 Aug 2020 12:46:48: start model_add_line... INFO @ Sat, 08 Aug 2020 12:46:48: start X-correlation... INFO @ Sat, 08 Aug 2020 12:46:48: end of X-cor INFO @ Sat, 08 Aug 2020 12:46:48: #2 finished! INFO @ Sat, 08 Aug 2020 12:46:48: #2 predicted fragment length is 201 bps INFO @ Sat, 08 Aug 2020 12:46:48: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 08 Aug 2020 12:46:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.10_model.r INFO @ Sat, 08 Aug 2020 12:46:48: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:46:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:46:48: 10000000 INFO @ Sat, 08 Aug 2020 12:46:54: 11000000 INFO @ Sat, 08 Aug 2020 12:46:59: 12000000 INFO @ Sat, 08 Aug 2020 12:47:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:47:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:47:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.05_summits.bed INFO @ Sat, 08 Aug 2020 12:47:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6021 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:47:05: 13000000 INFO @ Sat, 08 Aug 2020 12:47:10: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:47:16: 15000000 INFO @ Sat, 08 Aug 2020 12:47:16: #1 tag size is determined as 50 bps INFO @ Sat, 08 Aug 2020 12:47:16: #1 tag size = 50 INFO @ Sat, 08 Aug 2020 12:47:16: #1 total tags in treatment: 15117029 INFO @ Sat, 08 Aug 2020 12:47:16: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:47:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:47:16: #1 tags after filtering in treatment: 15117029 INFO @ Sat, 08 Aug 2020 12:47:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Aug 2020 12:47:16: #1 finished! INFO @ Sat, 08 Aug 2020 12:47:16: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:47:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:47:17: #2 number of paired peaks: 464 WARNING @ Sat, 08 Aug 2020 12:47:17: Fewer paired peaks (464) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 464 pairs to build model! INFO @ Sat, 08 Aug 2020 12:47:17: start model_add_line... INFO @ Sat, 08 Aug 2020 12:47:18: start X-correlation... INFO @ Sat, 08 Aug 2020 12:47:18: end of X-cor INFO @ Sat, 08 Aug 2020 12:47:18: #2 finished! INFO @ Sat, 08 Aug 2020 12:47:18: #2 predicted fragment length is 201 bps INFO @ Sat, 08 Aug 2020 12:47:18: #2 alternative fragment length(s) may be 201 bps INFO @ Sat, 08 Aug 2020 12:47:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.20_model.r INFO @ Sat, 08 Aug 2020 12:47:18: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:47:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:47:18: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:47:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:47:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:47:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.10_summits.bed INFO @ Sat, 08 Aug 2020 12:47:34: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4037 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:47:48: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:48:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:48:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:48:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7191474/SRX7191474.20_summits.bed INFO @ Sat, 08 Aug 2020 12:48:04: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2172 records, 4 fields): 3 millis CompletedMACS2peakCalling