Job ID = 6507739 SRX = SRX1995047 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T12:56:11 prefetch.2.10.7: 1) Downloading 'SRR3993979'... 2020-06-26T12:56:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T12:58:33 prefetch.2.10.7: HTTPS download succeed 2020-06-26T12:58:33 prefetch.2.10.7: 1) 'SRR3993979' was downloaded successfully Read 18591839 spots for SRR3993979/SRR3993979.sra Written 18591839 spots for SRR3993979/SRR3993979.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:26:51 18591839 reads; of these: 18591839 (100.00%) were paired; of these: 1311456 (7.05%) aligned concordantly 0 times 11888639 (63.95%) aligned concordantly exactly 1 time 5391744 (29.00%) aligned concordantly >1 times ---- 1311456 pairs aligned concordantly 0 times; of these: 472035 (35.99%) aligned discordantly 1 time ---- 839421 pairs aligned 0 times concordantly or discordantly; of these: 1678842 mates make up the pairs; of these: 1112120 (66.24%) aligned 0 times 265437 (15.81%) aligned exactly 1 time 301285 (17.95%) aligned >1 times 97.01% overall alignment rate Time searching: 00:26:52 Overall time: 00:26:52 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 3628283 / 17735743 = 0.2046 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 @ Fri, 26 Jun 2020 22:36:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.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 @ Fri, 26 Jun 2020 22:36:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:36:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:37:02: 1000000 INFO @ Fri, 26 Jun 2020 22:37:09: 2000000 INFO @ Fri, 26 Jun 2020 22:37:16: 3000000 INFO @ Fri, 26 Jun 2020 22:37:22: 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 @ Fri, 26 Jun 2020 22:37:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.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 @ Fri, 26 Jun 2020 22:37:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:37:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:37:29: 5000000 INFO @ Fri, 26 Jun 2020 22:37:32: 1000000 INFO @ Fri, 26 Jun 2020 22:37:36: 6000000 INFO @ Fri, 26 Jun 2020 22:37:40: 2000000 INFO @ Fri, 26 Jun 2020 22:37:44: 7000000 INFO @ Fri, 26 Jun 2020 22:37:47: 3000000 INFO @ Fri, 26 Jun 2020 22:37:51: 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 @ Fri, 26 Jun 2020 22:37:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.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 @ Fri, 26 Jun 2020 22:37:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 22:37:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 22:37:55: 4000000 INFO @ Fri, 26 Jun 2020 22:37:59: 9000000 INFO @ Fri, 26 Jun 2020 22:38:03: 1000000 INFO @ Fri, 26 Jun 2020 22:38:03: 5000000 INFO @ Fri, 26 Jun 2020 22:38:07: 10000000 INFO @ Fri, 26 Jun 2020 22:38:11: 2000000 INFO @ Fri, 26 Jun 2020 22:38:11: 6000000 INFO @ Fri, 26 Jun 2020 22:38:15: 11000000 INFO @ Fri, 26 Jun 2020 22:38:19: 3000000 INFO @ Fri, 26 Jun 2020 22:38:19: 7000000 INFO @ Fri, 26 Jun 2020 22:38:24: 12000000 INFO @ Fri, 26 Jun 2020 22:38:27: 4000000 INFO @ Fri, 26 Jun 2020 22:38:27: 8000000 INFO @ Fri, 26 Jun 2020 22:38:32: 13000000 INFO @ Fri, 26 Jun 2020 22:38:35: 5000000 INFO @ Fri, 26 Jun 2020 22:38:35: 9000000 INFO @ Fri, 26 Jun 2020 22:38:40: 14000000 INFO @ Fri, 26 Jun 2020 22:38:43: 6000000 INFO @ Fri, 26 Jun 2020 22:38:43: 10000000 INFO @ Fri, 26 Jun 2020 22:38:48: 15000000 INFO @ Fri, 26 Jun 2020 22:38:51: 7000000 INFO @ Fri, 26 Jun 2020 22:38:51: 11000000 INFO @ Fri, 26 Jun 2020 22:38:55: 16000000 INFO @ Fri, 26 Jun 2020 22:38:59: 8000000 INFO @ Fri, 26 Jun 2020 22:39:00: 12000000 INFO @ Fri, 26 Jun 2020 22:39:03: 17000000 INFO @ Fri, 26 Jun 2020 22:39:07: 9000000 INFO @ Fri, 26 Jun 2020 22:39:07: 13000000 INFO @ Fri, 26 Jun 2020 22:39:11: 18000000 INFO @ Fri, 26 Jun 2020 22:39:15: 14000000 INFO @ Fri, 26 Jun 2020 22:39:15: 10000000 INFO @ Fri, 26 Jun 2020 22:39:19: 19000000 INFO @ Fri, 26 Jun 2020 22:39:23: 15000000 INFO @ Fri, 26 Jun 2020 22:39:23: 11000000 INFO @ Fri, 26 Jun 2020 22:39:26: 20000000 INFO @ Fri, 26 Jun 2020 22:39:31: 16000000 INFO @ Fri, 26 Jun 2020 22:39:31: 12000000 INFO @ Fri, 26 Jun 2020 22:39:34: 21000000 INFO @ Fri, 26 Jun 2020 22:39:38: 17000000 INFO @ Fri, 26 Jun 2020 22:39:39: 13000000 INFO @ Fri, 26 Jun 2020 22:39:42: 22000000 INFO @ Fri, 26 Jun 2020 22:39:46: 18000000 INFO @ Fri, 26 Jun 2020 22:39:47: 14000000 INFO @ Fri, 26 Jun 2020 22:39:49: 23000000 INFO @ Fri, 26 Jun 2020 22:39:53: 19000000 INFO @ Fri, 26 Jun 2020 22:39:55: 15000000 INFO @ Fri, 26 Jun 2020 22:39:57: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 22:40:01: 20000000 INFO @ Fri, 26 Jun 2020 22:40:03: 16000000 INFO @ Fri, 26 Jun 2020 22:40:05: 25000000 INFO @ Fri, 26 Jun 2020 22:40:09: 21000000 INFO @ Fri, 26 Jun 2020 22:40:11: 17000000 INFO @ Fri, 26 Jun 2020 22:40:12: 26000000 INFO @ Fri, 26 Jun 2020 22:40:16: 22000000 INFO @ Fri, 26 Jun 2020 22:40:19: 18000000 INFO @ Fri, 26 Jun 2020 22:40:20: 27000000 INFO @ Fri, 26 Jun 2020 22:40:24: 23000000 INFO @ Fri, 26 Jun 2020 22:40:27: 19000000 INFO @ Fri, 26 Jun 2020 22:40:27: 28000000 INFO @ Fri, 26 Jun 2020 22:40:31: 24000000 INFO @ Fri, 26 Jun 2020 22:40:33: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:40:33: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:40:33: #1 total tags in treatment: 13692247 INFO @ Fri, 26 Jun 2020 22:40:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:40:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:40:34: #1 tags after filtering in treatment: 10772828 INFO @ Fri, 26 Jun 2020 22:40:34: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 26 Jun 2020 22:40:34: #1 finished! INFO @ Fri, 26 Jun 2020 22:40:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:40:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:40:35: #2 number of paired peaks: 1985 INFO @ Fri, 26 Jun 2020 22:40:35: start model_add_line... INFO @ Fri, 26 Jun 2020 22:40:35: start X-correlation... INFO @ Fri, 26 Jun 2020 22:40:35: end of X-cor INFO @ Fri, 26 Jun 2020 22:40:35: #2 finished! INFO @ Fri, 26 Jun 2020 22:40:35: #2 predicted fragment length is 185 bps INFO @ Fri, 26 Jun 2020 22:40:35: #2 alternative fragment length(s) may be 185 bps INFO @ Fri, 26 Jun 2020 22:40:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.05_model.r INFO @ Fri, 26 Jun 2020 22:40:35: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:40:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:40:35: 20000000 INFO @ Fri, 26 Jun 2020 22:40:39: 25000000 INFO @ Fri, 26 Jun 2020 22:40:43: 21000000 INFO @ Fri, 26 Jun 2020 22:40:46: 26000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 22:40:50: 22000000 INFO @ Fri, 26 Jun 2020 22:40:53: 27000000 INFO @ Fri, 26 Jun 2020 22:40:58: 23000000 INFO @ Fri, 26 Jun 2020 22:41:01: 28000000 INFO @ Fri, 26 Jun 2020 22:41:06: 24000000 INFO @ Fri, 26 Jun 2020 22:41:07: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:41:07: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:41:07: #1 total tags in treatment: 13692247 INFO @ Fri, 26 Jun 2020 22:41:07: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:41:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:41:07: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:41:07: #1 tags after filtering in treatment: 10772828 INFO @ Fri, 26 Jun 2020 22:41:07: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 26 Jun 2020 22:41:07: #1 finished! INFO @ Fri, 26 Jun 2020 22:41:07: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:41:07: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:41:08: #2 number of paired peaks: 1985 INFO @ Fri, 26 Jun 2020 22:41:08: start model_add_line... INFO @ Fri, 26 Jun 2020 22:41:08: start X-correlation... INFO @ Fri, 26 Jun 2020 22:41:08: end of X-cor INFO @ Fri, 26 Jun 2020 22:41:08: #2 finished! INFO @ Fri, 26 Jun 2020 22:41:08: #2 predicted fragment length is 185 bps INFO @ Fri, 26 Jun 2020 22:41:08: #2 alternative fragment length(s) may be 185 bps INFO @ Fri, 26 Jun 2020 22:41:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.10_model.r INFO @ Fri, 26 Jun 2020 22:41:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:41:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:41:13: 25000000 INFO @ Fri, 26 Jun 2020 22:41:20: 26000000 INFO @ Fri, 26 Jun 2020 22:41:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.05_peaks.xls INFO @ Fri, 26 Jun 2020 22:41:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:41:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.05_summits.bed INFO @ Fri, 26 Jun 2020 22:41:21: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4309 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:41:26: 27000000 INFO @ Fri, 26 Jun 2020 22:41:33: 28000000 INFO @ Fri, 26 Jun 2020 22:41:38: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:41:39: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 22:41:39: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 22:41:39: #1 total tags in treatment: 13692247 INFO @ Fri, 26 Jun 2020 22:41:39: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 22:41:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 22:41:39: #1 tags after filtering in treatment: 10772828 INFO @ Fri, 26 Jun 2020 22:41:39: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 26 Jun 2020 22:41:39: #1 finished! INFO @ Fri, 26 Jun 2020 22:41:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 22:41:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 22:41:40: #2 number of paired peaks: 1985 INFO @ Fri, 26 Jun 2020 22:41:40: start model_add_line... INFO @ Fri, 26 Jun 2020 22:41:40: start X-correlation... INFO @ Fri, 26 Jun 2020 22:41:40: end of X-cor INFO @ Fri, 26 Jun 2020 22:41:40: #2 finished! INFO @ Fri, 26 Jun 2020 22:41:40: #2 predicted fragment length is 185 bps INFO @ Fri, 26 Jun 2020 22:41:40: #2 alternative fragment length(s) may be 185 bps INFO @ Fri, 26 Jun 2020 22:41:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.20_model.r INFO @ Fri, 26 Jun 2020 22:41:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 22:41:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 22:41:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.10_peaks.xls INFO @ Fri, 26 Jun 2020 22:41:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:41:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.10_summits.bed INFO @ Fri, 26 Jun 2020 22:41:51: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2814 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 22:42:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 22:42:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.20_peaks.xls INFO @ Fri, 26 Jun 2020 22:42:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 22:42:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1995047/SRX1995047.20_summits.bed INFO @ Fri, 26 Jun 2020 22:42:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1511 records, 4 fields): 3 millis CompletedMACS2peakCalling