Job ID = 6367022 SRX = SRX2710283 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-15T23:10:46 prefetch.2.10.7: 1) Downloading 'SRR5418737'... 2020-06-15T23:10:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:17:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:17:00 prefetch.2.10.7: 1) 'SRR5418737' was downloaded successfully Read 65854207 spots for SRR5418737/SRR5418737.sra Written 65854207 spots for SRR5418737/SRR5418737.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: 00:22:27 65854207 reads; of these: 65854207 (100.00%) were unpaired; of these: 4543712 (6.90%) aligned 0 times 21622029 (32.83%) aligned exactly 1 time 39688466 (60.27%) aligned >1 times 93.10% overall alignment rate Time searching: 00:22:27 Overall time: 00:22:27 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 28 files... [bam_rmdupse_core] 43066288 / 61310495 = 0.7024 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 @ Tue, 16 Jun 2020 08:54:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:54:33: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:54:33: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:54:40: 1000000 INFO @ Tue, 16 Jun 2020 08:54:46: 2000000 INFO @ Tue, 16 Jun 2020 08:54:52: 3000000 INFO @ Tue, 16 Jun 2020 08:54:58: 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 @ Tue, 16 Jun 2020 08:55:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:55:03: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:03: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:55:04: 5000000 INFO @ Tue, 16 Jun 2020 08:55:10: 6000000 INFO @ Tue, 16 Jun 2020 08:55:10: 1000000 INFO @ Tue, 16 Jun 2020 08:55:16: 7000000 INFO @ Tue, 16 Jun 2020 08:55:16: 2000000 INFO @ Tue, 16 Jun 2020 08:55:22: 3000000 INFO @ Tue, 16 Jun 2020 08:55:22: 8000000 INFO @ Tue, 16 Jun 2020 08:55:28: 9000000 INFO @ Tue, 16 Jun 2020 08:55:29: 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 @ Tue, 16 Jun 2020 08:55:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 08:55:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:55:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:55:35: 10000000 INFO @ Tue, 16 Jun 2020 08:55:35: 5000000 INFO @ Tue, 16 Jun 2020 08:55:40: 1000000 INFO @ Tue, 16 Jun 2020 08:55:41: 11000000 INFO @ Tue, 16 Jun 2020 08:55:41: 6000000 INFO @ Tue, 16 Jun 2020 08:55:46: 2000000 INFO @ Tue, 16 Jun 2020 08:55:47: 12000000 INFO @ Tue, 16 Jun 2020 08:55:48: 7000000 INFO @ Tue, 16 Jun 2020 08:55:51: 3000000 INFO @ Tue, 16 Jun 2020 08:55:54: 13000000 INFO @ Tue, 16 Jun 2020 08:55:54: 8000000 INFO @ Tue, 16 Jun 2020 08:55:57: 4000000 INFO @ Tue, 16 Jun 2020 08:56:00: 14000000 INFO @ Tue, 16 Jun 2020 08:56:01: 9000000 INFO @ Tue, 16 Jun 2020 08:56:03: 5000000 INFO @ Tue, 16 Jun 2020 08:56:06: 15000000 INFO @ Tue, 16 Jun 2020 08:56:07: 10000000 INFO @ Tue, 16 Jun 2020 08:56:08: 6000000 INFO @ Tue, 16 Jun 2020 08:56:13: 16000000 INFO @ Tue, 16 Jun 2020 08:56:14: 11000000 INFO @ Tue, 16 Jun 2020 08:56:14: 7000000 INFO @ Tue, 16 Jun 2020 08:56:19: 17000000 INFO @ Tue, 16 Jun 2020 08:56:20: 8000000 INFO @ Tue, 16 Jun 2020 08:56:20: 12000000 INFO @ Tue, 16 Jun 2020 08:56:25: 9000000 INFO @ Tue, 16 Jun 2020 08:56:26: 18000000 INFO @ Tue, 16 Jun 2020 08:56:27: 13000000 INFO @ Tue, 16 Jun 2020 08:56:27: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:56:27: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:56:27: #1 total tags in treatment: 18244207 INFO @ Tue, 16 Jun 2020 08:56:27: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:56:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:56:28: #1 tags after filtering in treatment: 18244207 INFO @ Tue, 16 Jun 2020 08:56:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:56:28: #1 finished! INFO @ Tue, 16 Jun 2020 08:56:28: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:56:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:56:29: #2 number of paired peaks: 1871 INFO @ Tue, 16 Jun 2020 08:56:29: start model_add_line... INFO @ Tue, 16 Jun 2020 08:56:29: start X-correlation... INFO @ Tue, 16 Jun 2020 08:56:29: end of X-cor INFO @ Tue, 16 Jun 2020 08:56:29: #2 finished! INFO @ Tue, 16 Jun 2020 08:56:29: #2 predicted fragment length is 102 bps INFO @ Tue, 16 Jun 2020 08:56:29: #2 alternative fragment length(s) may be 4,102 bps INFO @ Tue, 16 Jun 2020 08:56:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.05_model.r INFO @ Tue, 16 Jun 2020 08:56:29: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:56:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:56:31: 10000000 INFO @ Tue, 16 Jun 2020 08:56:33: 14000000 INFO @ Tue, 16 Jun 2020 08:56:37: 11000000 INFO @ Tue, 16 Jun 2020 08:56:39: 15000000 INFO @ Tue, 16 Jun 2020 08:56:42: 12000000 INFO @ Tue, 16 Jun 2020 08:56:46: 16000000 INFO @ Tue, 16 Jun 2020 08:56:48: 13000000 INFO @ Tue, 16 Jun 2020 08:56:52: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:56:54: 14000000 INFO @ Tue, 16 Jun 2020 08:56:59: 18000000 INFO @ Tue, 16 Jun 2020 08:56:59: 15000000 INFO @ Tue, 16 Jun 2020 08:57:01: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:57:01: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:57:01: #1 total tags in treatment: 18244207 INFO @ Tue, 16 Jun 2020 08:57:01: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:57:01: #1 tags after filtering in treatment: 18244207 INFO @ Tue, 16 Jun 2020 08:57:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:01: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:01: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:03: #2 number of paired peaks: 1871 INFO @ Tue, 16 Jun 2020 08:57:03: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:03: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:03: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:03: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:03: #2 predicted fragment length is 102 bps INFO @ Tue, 16 Jun 2020 08:57:03: #2 alternative fragment length(s) may be 4,102 bps INFO @ Tue, 16 Jun 2020 08:57:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.10_model.r INFO @ Tue, 16 Jun 2020 08:57:03: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:57:05: 16000000 INFO @ Tue, 16 Jun 2020 08:57:11: 17000000 INFO @ Tue, 16 Jun 2020 08:57:11: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:57:16: 18000000 INFO @ Tue, 16 Jun 2020 08:57:18: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 08:57:18: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 08:57:18: #1 total tags in treatment: 18244207 INFO @ Tue, 16 Jun 2020 08:57:18: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:57:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 08:57:18: #1 tags after filtering in treatment: 18244207 INFO @ Tue, 16 Jun 2020 08:57:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 08:57:18: #1 finished! INFO @ Tue, 16 Jun 2020 08:57:18: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:57:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:57:20: #2 number of paired peaks: 1871 INFO @ Tue, 16 Jun 2020 08:57:20: start model_add_line... INFO @ Tue, 16 Jun 2020 08:57:20: start X-correlation... INFO @ Tue, 16 Jun 2020 08:57:20: end of X-cor INFO @ Tue, 16 Jun 2020 08:57:20: #2 finished! INFO @ Tue, 16 Jun 2020 08:57:20: #2 predicted fragment length is 102 bps INFO @ Tue, 16 Jun 2020 08:57:20: #2 alternative fragment length(s) may be 4,102 bps INFO @ Tue, 16 Jun 2020 08:57:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.20_model.r INFO @ Tue, 16 Jun 2020 08:57:20: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:57:20: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:57:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:57:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:57:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.05_summits.bed INFO @ Tue, 16 Jun 2020 08:57:32: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (25147 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:57:44: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:58:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.10_summits.bed INFO @ Tue, 16 Jun 2020 08:58:05: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (18425 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:58:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:58:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:58:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2710283/SRX2710283.20_summits.bed INFO @ Tue, 16 Jun 2020 08:58:22: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (10619 records, 4 fields): 13 millis CompletedMACS2peakCalling