Job ID = 14518032 SRX = SRX10533682 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-01-14T22:39:56 prefetch.2.10.7: 1) Downloading 'SRR14165462'... 2022-01-14T22:39:56 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:40:07 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:40:07 prefetch.2.10.7: 'SRR14165462' is valid 2022-01-14T22:40:07 prefetch.2.10.7: 1) 'SRR14165462' was downloaded successfully 2022-01-14T22:40:07 prefetch.2.10.7: 'SRR14165462' has 0 unresolved dependencies Read 4000000 spots for SRR14165462/SRR14165462.sra Written 4000000 spots for SRR14165462/SRR14165462.sra Read 4000000 spots for SRR14165463/SRR14165463.sra Written 4000000 spots for SRR14165463/SRR14165463.sra Read 4000000 spots for SRR14165464/SRR14165464.sra Written 4000000 spots for SRR14165464/SRR14165464.sra Read 4000000 spots for SRR14165465/SRR14165465.sra Written 4000000 spots for SRR14165465/SRR14165465.sra Read 4000000 spots for SRR14165466/SRR14165466.sra Written 4000000 spots for SRR14165466/SRR14165466.sra 2022-01-14T22:41:26 prefetch.2.10.7: 1) Downloading 'SRR14165467'... 2022-01-14T22:41:26 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:41:37 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:41:38 prefetch.2.10.7: 'SRR14165467' is valid 2022-01-14T22:41:38 prefetch.2.10.7: 1) 'SRR14165467' was downloaded successfully 2022-01-14T22:41:38 prefetch.2.10.7: 'SRR14165467' has 0 unresolved dependencies Read 4000000 spots for SRR14165467/SRR14165467.sra Written 4000000 spots for SRR14165467/SRR14165467.sra 2022-01-14T22:41:58 prefetch.2.10.7: 1) Downloading 'SRR14165468'... 2022-01-14T22:41:58 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:42:09 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:42:09 prefetch.2.10.7: 'SRR14165468' is valid 2022-01-14T22:42:09 prefetch.2.10.7: 1) 'SRR14165468' was downloaded successfully 2022-01-14T22:42:09 prefetch.2.10.7: 'SRR14165468' has 0 unresolved dependencies Read 4000000 spots for SRR14165468/SRR14165468.sra Written 4000000 spots for SRR14165468/SRR14165468.sra Read 4000000 spots for SRR14165469/SRR14165469.sra Written 4000000 spots for SRR14165469/SRR14165469.sra 2022-01-14T22:42:42 prefetch.2.10.7: 1) Downloading 'SRR14165470'... 2022-01-14T22:42:42 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:42:52 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:42:52 prefetch.2.10.7: 'SRR14165470' is valid 2022-01-14T22:42:52 prefetch.2.10.7: 1) 'SRR14165470' was downloaded successfully 2022-01-14T22:42:52 prefetch.2.10.7: 'SRR14165470' has 0 unresolved dependencies Read 3971568 spots for SRR14165470/SRR14165470.sra Written 3971568 spots for SRR14165470/SRR14165470.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:14:08 35971568 reads; of these: 35971568 (100.00%) were unpaired; of these: 19966500 (55.51%) aligned 0 times 13050868 (36.28%) aligned exactly 1 time 2954200 (8.21%) aligned >1 times 44.49% overall alignment rate Time searching: 00:14:12 Overall time: 00:14:12 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 5592652 / 16005068 = 0.3494 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 08:01:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 15 Jan 2022 08:01:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 08:01:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 08:01:30: 1000000 INFO @ Sat, 15 Jan 2022 08:01:37: 2000000 INFO @ Sat, 15 Jan 2022 08:01:43: 3000000 INFO @ Sat, 15 Jan 2022 08:01:49: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 08:01:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 15 Jan 2022 08:01:54: #1 read tag files... INFO @ Sat, 15 Jan 2022 08:01:54: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 08:01:56: 5000000 INFO @ Sat, 15 Jan 2022 08:02:00: 1000000 INFO @ Sat, 15 Jan 2022 08:02:02: 6000000 INFO @ Sat, 15 Jan 2022 08:02:06: 2000000 INFO @ Sat, 15 Jan 2022 08:02:09: 7000000 INFO @ Sat, 15 Jan 2022 08:02:13: 3000000 INFO @ Sat, 15 Jan 2022 08:02:16: 8000000 INFO @ Sat, 15 Jan 2022 08:02:19: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 08:02:23: 9000000 INFO @ Sat, 15 Jan 2022 08:02:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 15 Jan 2022 08:02:24: #1 read tag files... INFO @ Sat, 15 Jan 2022 08:02:24: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 08:02:25: 5000000 INFO @ Sat, 15 Jan 2022 08:02:29: 10000000 INFO @ Sat, 15 Jan 2022 08:02:30: 1000000 INFO @ Sat, 15 Jan 2022 08:02:32: 6000000 INFO @ Sat, 15 Jan 2022 08:02:32: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 08:02:32: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 08:02:32: #1 total tags in treatment: 10412416 INFO @ Sat, 15 Jan 2022 08:02:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 08:02:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 08:02:33: #1 tags after filtering in treatment: 10412162 INFO @ Sat, 15 Jan 2022 08:02:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 08:02:33: #1 finished! INFO @ Sat, 15 Jan 2022 08:02:33: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 08:02:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 08:02:36: #2 number of paired peaks: 75647 INFO @ Sat, 15 Jan 2022 08:02:36: start model_add_line... INFO @ Sat, 15 Jan 2022 08:02:36: start X-correlation... INFO @ Sat, 15 Jan 2022 08:02:36: end of X-cor INFO @ Sat, 15 Jan 2022 08:02:36: #2 finished! INFO @ Sat, 15 Jan 2022 08:02:36: #2 predicted fragment length is 297 bps INFO @ Sat, 15 Jan 2022 08:02:36: #2 alternative fragment length(s) may be 297 bps INFO @ Sat, 15 Jan 2022 08:02:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.05_model.r INFO @ Sat, 15 Jan 2022 08:02:36: #3 Call peaks... INFO @ Sat, 15 Jan 2022 08:02:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 08:02:36: 2000000 INFO @ Sat, 15 Jan 2022 08:02:38: 7000000 INFO @ Sat, 15 Jan 2022 08:02:43: 3000000 INFO @ Sat, 15 Jan 2022 08:02:44: 8000000 INFO @ Sat, 15 Jan 2022 08:02:49: 4000000 INFO @ Sat, 15 Jan 2022 08:02:50: 9000000 INFO @ Sat, 15 Jan 2022 08:02:55: 5000000 INFO @ Sat, 15 Jan 2022 08:02:56: 10000000 INFO @ Sat, 15 Jan 2022 08:02:59: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 08:02:59: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 08:02:59: #1 total tags in treatment: 10412416 INFO @ Sat, 15 Jan 2022 08:02:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 08:02:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 08:02:59: #1 tags after filtering in treatment: 10412162 INFO @ Sat, 15 Jan 2022 08:02:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 08:02:59: #1 finished! INFO @ Sat, 15 Jan 2022 08:02:59: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 08:02:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 08:03:00: 6000000 INFO @ Sat, 15 Jan 2022 08:03:02: #2 number of paired peaks: 75647 INFO @ Sat, 15 Jan 2022 08:03:02: start model_add_line... INFO @ Sat, 15 Jan 2022 08:03:02: start X-correlation... INFO @ Sat, 15 Jan 2022 08:03:02: end of X-cor INFO @ Sat, 15 Jan 2022 08:03:02: #2 finished! INFO @ Sat, 15 Jan 2022 08:03:02: #2 predicted fragment length is 297 bps INFO @ Sat, 15 Jan 2022 08:03:02: #2 alternative fragment length(s) may be 297 bps INFO @ Sat, 15 Jan 2022 08:03:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.10_model.r INFO @ Sat, 15 Jan 2022 08:03:02: #3 Call peaks... INFO @ Sat, 15 Jan 2022 08:03:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 08:03:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 08:03:06: 7000000 INFO @ Sat, 15 Jan 2022 08:03:11: 8000000 INFO @ Sat, 15 Jan 2022 08:03:17: 9000000 INFO @ Sat, 15 Jan 2022 08:03:17: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.05_peaks.xls INFO @ Sat, 15 Jan 2022 08:03:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 08:03:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.05_summits.bed INFO @ Sat, 15 Jan 2022 08:03:17: Done! pass1 - making usageList (74 chroms): 1 millis pass2 - checking and writing primary data (3109 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 08:03:22: 10000000 INFO @ Sat, 15 Jan 2022 08:03:25: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 08:03:25: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 08:03:25: #1 total tags in treatment: 10412416 INFO @ Sat, 15 Jan 2022 08:03:25: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 08:03:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 08:03:25: #1 tags after filtering in treatment: 10412162 INFO @ Sat, 15 Jan 2022 08:03:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 08:03:25: #1 finished! INFO @ Sat, 15 Jan 2022 08:03:25: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 08:03:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 08:03:28: #2 number of paired peaks: 75647 INFO @ Sat, 15 Jan 2022 08:03:28: start model_add_line... INFO @ Sat, 15 Jan 2022 08:03:28: start X-correlation... INFO @ Sat, 15 Jan 2022 08:03:28: end of X-cor INFO @ Sat, 15 Jan 2022 08:03:28: #2 finished! INFO @ Sat, 15 Jan 2022 08:03:28: #2 predicted fragment length is 297 bps INFO @ Sat, 15 Jan 2022 08:03:28: #2 alternative fragment length(s) may be 297 bps INFO @ Sat, 15 Jan 2022 08:03:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.20_model.r INFO @ Sat, 15 Jan 2022 08:03:28: #3 Call peaks... INFO @ Sat, 15 Jan 2022 08:03:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 08:03:31: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 08:03:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.10_peaks.xls INFO @ Sat, 15 Jan 2022 08:03:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 08:03:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.10_summits.bed INFO @ Sat, 15 Jan 2022 08:03:45: Done! pass1 - making usageList (56 chroms): 1 millis pass2 - checking and writing primary data (1262 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 08:03:58: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 08:04:12: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.20_peaks.xls INFO @ Sat, 15 Jan 2022 08:04:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 08:04:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533682/SRX10533682.20_summits.bed INFO @ Sat, 15 Jan 2022 08:04:12: Done! pass1 - making usageList (49 chroms): 0 millis pass2 - checking and writing primary data (443 records, 4 fields): 5 millis CompletedMACS2peakCalling