Job ID = 6507738 SRX = SRX1995035 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:48:00 prefetch.2.10.7: 1) Downloading 'SRR3993967'... 2020-06-26T13:48:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:50:24 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:50:24 prefetch.2.10.7: 1) 'SRR3993967' was downloaded successfully Read 18653692 spots for SRR3993967/SRR3993967.sra Written 18653692 spots for SRR3993967/SRR3993967.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: 00:25:16 18653692 reads; of these: 18653692 (100.00%) were paired; of these: 1314817 (7.05%) aligned concordantly 0 times 11931981 (63.97%) aligned concordantly exactly 1 time 5406894 (28.99%) aligned concordantly >1 times ---- 1314817 pairs aligned concordantly 0 times; of these: 478152 (36.37%) aligned discordantly 1 time ---- 836665 pairs aligned 0 times concordantly or discordantly; of these: 1673330 mates make up the pairs; of these: 1106411 (66.12%) aligned 0 times 265267 (15.85%) aligned exactly 1 time 301652 (18.03%) aligned >1 times 97.03% overall alignment rate Time searching: 00:25:16 Overall time: 00:25:16 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] 3653391 / 17799919 = 0.2052 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 23:26:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.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 23:26:38: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:26:38: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:26:43: 1000000 INFO @ Fri, 26 Jun 2020 23:26:49: 2000000 INFO @ Fri, 26 Jun 2020 23:26:54: 3000000 INFO @ Fri, 26 Jun 2020 23:26:59: 4000000 INFO @ Fri, 26 Jun 2020 23:27:05: 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 @ Fri, 26 Jun 2020 23:27:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.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 23:27:08: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:27:08: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:27:10: 6000000 INFO @ Fri, 26 Jun 2020 23:27:14: 1000000 INFO @ Fri, 26 Jun 2020 23:27:16: 7000000 INFO @ Fri, 26 Jun 2020 23:27:19: 2000000 INFO @ Fri, 26 Jun 2020 23:27:22: 8000000 INFO @ Fri, 26 Jun 2020 23:27:25: 3000000 INFO @ Fri, 26 Jun 2020 23:27:28: 9000000 INFO @ Fri, 26 Jun 2020 23:27:31: 4000000 INFO @ Fri, 26 Jun 2020 23:27:33: 10000000 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 23:27:36: 5000000 INFO @ Fri, 26 Jun 2020 23:27:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.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 23:27:38: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:27:38: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:27:39: 11000000 INFO @ Fri, 26 Jun 2020 23:27:42: 6000000 INFO @ Fri, 26 Jun 2020 23:27:45: 12000000 INFO @ Fri, 26 Jun 2020 23:27:45: 1000000 INFO @ Fri, 26 Jun 2020 23:27:48: 7000000 INFO @ Fri, 26 Jun 2020 23:27:51: 13000000 INFO @ Fri, 26 Jun 2020 23:27:51: 2000000 INFO @ Fri, 26 Jun 2020 23:27:54: 8000000 INFO @ Fri, 26 Jun 2020 23:27:57: 14000000 INFO @ Fri, 26 Jun 2020 23:27:57: 3000000 INFO @ Fri, 26 Jun 2020 23:28:00: 9000000 INFO @ Fri, 26 Jun 2020 23:28:03: 15000000 INFO @ Fri, 26 Jun 2020 23:28:04: 4000000 INFO @ Fri, 26 Jun 2020 23:28:06: 10000000 INFO @ Fri, 26 Jun 2020 23:28:09: 16000000 INFO @ Fri, 26 Jun 2020 23:28:10: 5000000 INFO @ Fri, 26 Jun 2020 23:28:13: 11000000 INFO @ Fri, 26 Jun 2020 23:28:15: 17000000 INFO @ Fri, 26 Jun 2020 23:28:16: 6000000 INFO @ Fri, 26 Jun 2020 23:28:19: 12000000 INFO @ Fri, 26 Jun 2020 23:28:21: 18000000 INFO @ Fri, 26 Jun 2020 23:28:22: 7000000 INFO @ Fri, 26 Jun 2020 23:28:25: 13000000 INFO @ Fri, 26 Jun 2020 23:28:27: 19000000 INFO @ Fri, 26 Jun 2020 23:28:28: 8000000 INFO @ Fri, 26 Jun 2020 23:28:31: 14000000 INFO @ Fri, 26 Jun 2020 23:28:33: 20000000 INFO @ Fri, 26 Jun 2020 23:28:35: 9000000 INFO @ Fri, 26 Jun 2020 23:28:37: 15000000 INFO @ Fri, 26 Jun 2020 23:28:39: 21000000 INFO @ Fri, 26 Jun 2020 23:28:41: 10000000 INFO @ Fri, 26 Jun 2020 23:28:43: 16000000 INFO @ Fri, 26 Jun 2020 23:28:45: 22000000 INFO @ Fri, 26 Jun 2020 23:28:47: 11000000 INFO @ Fri, 26 Jun 2020 23:28:49: 17000000 INFO @ Fri, 26 Jun 2020 23:28:51: 23000000 INFO @ Fri, 26 Jun 2020 23:28:53: 12000000 INFO @ Fri, 26 Jun 2020 23:28:55: 18000000 INFO @ Fri, 26 Jun 2020 23:28:57: 24000000 INFO @ Fri, 26 Jun 2020 23:28:59: 13000000 INFO @ Fri, 26 Jun 2020 23:29:01: 19000000 INFO @ Fri, 26 Jun 2020 23:29:03: 25000000 INFO @ Fri, 26 Jun 2020 23:29:05: 14000000 INFO @ Fri, 26 Jun 2020 23:29:07: 20000000 INFO @ Fri, 26 Jun 2020 23:29:09: 26000000 INFO @ Fri, 26 Jun 2020 23:29:11: 15000000 INFO @ Fri, 26 Jun 2020 23:29:13: 21000000 INFO @ Fri, 26 Jun 2020 23:29:15: 27000000 INFO @ Fri, 26 Jun 2020 23:29:16: 16000000 INFO @ Fri, 26 Jun 2020 23:29:18: 22000000 INFO @ Fri, 26 Jun 2020 23:29:21: 28000000 INFO @ Fri, 26 Jun 2020 23:29:22: 17000000 INFO @ Fri, 26 Jun 2020 23:29:24: 23000000 INFO @ Fri, 26 Jun 2020 23:29:26: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:29:26: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:29:26: #1 total tags in treatment: 13726162 INFO @ Fri, 26 Jun 2020 23:29:26: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:29:26: #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 23:29:26: #1 tags after filtering in treatment: 10799816 INFO @ Fri, 26 Jun 2020 23:29:26: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 26 Jun 2020 23:29:26: #1 finished! INFO @ Fri, 26 Jun 2020 23:29:26: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:29:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:29:27: #2 number of paired peaks: 1970 INFO @ Fri, 26 Jun 2020 23:29:27: start model_add_line... INFO @ Fri, 26 Jun 2020 23:29:27: start X-correlation... INFO @ Fri, 26 Jun 2020 23:29:27: end of X-cor INFO @ Fri, 26 Jun 2020 23:29:27: #2 finished! INFO @ Fri, 26 Jun 2020 23:29:27: #2 predicted fragment length is 183 bps INFO @ Fri, 26 Jun 2020 23:29:27: #2 alternative fragment length(s) may be 183 bps INFO @ Fri, 26 Jun 2020 23:29:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.05_model.r INFO @ Fri, 26 Jun 2020 23:29:27: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:29:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:29:28: 18000000 INFO @ Fri, 26 Jun 2020 23:29:30: 24000000 INFO @ Fri, 26 Jun 2020 23:29:34: 19000000 INFO @ Fri, 26 Jun 2020 23:29:35: 25000000 INFO @ Fri, 26 Jun 2020 23:29:40: 20000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:29:41: 26000000 INFO @ Fri, 26 Jun 2020 23:29:46: 21000000 INFO @ Fri, 26 Jun 2020 23:29:47: 27000000 INFO @ Fri, 26 Jun 2020 23:29:51: 22000000 INFO @ Fri, 26 Jun 2020 23:29:53: 28000000 INFO @ Fri, 26 Jun 2020 23:29:57: 23000000 INFO @ Fri, 26 Jun 2020 23:29:58: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:29:58: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:29:58: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:29:58: #1 total tags in treatment: 13726162 INFO @ Fri, 26 Jun 2020 23:29:58: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:29:58: #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 23:29:59: #1 tags after filtering in treatment: 10799816 INFO @ Fri, 26 Jun 2020 23:29:59: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 26 Jun 2020 23:29:59: #1 finished! INFO @ Fri, 26 Jun 2020 23:29:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:29:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:30:00: #2 number of paired peaks: 1970 INFO @ Fri, 26 Jun 2020 23:30:00: start model_add_line... INFO @ Fri, 26 Jun 2020 23:30:00: start X-correlation... INFO @ Fri, 26 Jun 2020 23:30:00: end of X-cor INFO @ Fri, 26 Jun 2020 23:30:00: #2 finished! INFO @ Fri, 26 Jun 2020 23:30:00: #2 predicted fragment length is 183 bps INFO @ Fri, 26 Jun 2020 23:30:00: #2 alternative fragment length(s) may be 183 bps INFO @ Fri, 26 Jun 2020 23:30:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.10_model.r INFO @ Fri, 26 Jun 2020 23:30:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:30:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:30:03: 24000000 INFO @ Fri, 26 Jun 2020 23:30:08: 25000000 INFO @ Fri, 26 Jun 2020 23:30:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:30:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:30:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.05_summits.bed INFO @ Fri, 26 Jun 2020 23:30:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4374 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:30:13: 26000000 INFO @ Fri, 26 Jun 2020 23:30:19: 27000000 INFO @ Fri, 26 Jun 2020 23:30:24: 28000000 INFO @ Fri, 26 Jun 2020 23:30:29: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:30:29: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:30:29: #1 total tags in treatment: 13726162 INFO @ Fri, 26 Jun 2020 23:30:29: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:30:29: #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 23:30:29: #1 tags after filtering in treatment: 10799816 INFO @ Fri, 26 Jun 2020 23:30:29: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 26 Jun 2020 23:30:29: #1 finished! INFO @ Fri, 26 Jun 2020 23:30:29: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:30:29: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:30:30: #2 number of paired peaks: 1970 INFO @ Fri, 26 Jun 2020 23:30:30: start model_add_line... INFO @ Fri, 26 Jun 2020 23:30:30: start X-correlation... INFO @ Fri, 26 Jun 2020 23:30:30: end of X-cor INFO @ Fri, 26 Jun 2020 23:30:30: #2 finished! INFO @ Fri, 26 Jun 2020 23:30:30: #2 predicted fragment length is 183 bps INFO @ Fri, 26 Jun 2020 23:30:30: #2 alternative fragment length(s) may be 183 bps INFO @ Fri, 26 Jun 2020 23:30:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.20_model.r INFO @ Fri, 26 Jun 2020 23:30:30: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:30:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:30:30: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:30:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:30:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:30:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.10_summits.bed INFO @ Fri, 26 Jun 2020 23:30:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2810 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:31:01: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:31:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:31:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:31:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1995035/SRX1995035.20_summits.bed INFO @ Fri, 26 Jun 2020 23:31:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1495 records, 4 fields): 3 millis CompletedMACS2peakCalling