Job ID = 6507740 SRX = SRX1995058 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:44:31 prefetch.2.10.7: 1) Downloading 'SRR3993990'... 2020-06-26T13:44:31 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:50:15 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:50:15 prefetch.2.10.7: 1) 'SRR3993990' was downloaded successfully Read 33075103 spots for SRR3993990/SRR3993990.sra Written 33075103 spots for SRR3993990/SRR3993990.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: 00:29:33 33075103 reads; of these: 33075103 (100.00%) were paired; of these: 3887045 (11.75%) aligned concordantly 0 times 25134135 (75.99%) aligned concordantly exactly 1 time 4053923 (12.26%) aligned concordantly >1 times ---- 3887045 pairs aligned concordantly 0 times; of these: 944686 (24.30%) aligned discordantly 1 time ---- 2942359 pairs aligned 0 times concordantly or discordantly; of these: 5884718 mates make up the pairs; of these: 3940934 (66.97%) aligned 0 times 1409950 (23.96%) aligned exactly 1 time 533834 (9.07%) aligned >1 times 94.04% overall alignment rate Time searching: 00:29:33 Overall time: 00:29:33 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_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] 11915094 / 30087478 = 0.3960 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 23:37:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.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 23:37:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:37:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:37:42: 1000000 INFO @ Fri, 26 Jun 2020 23:37:47: 2000000 INFO @ Fri, 26 Jun 2020 23:37:52: 3000000 INFO @ Fri, 26 Jun 2020 23:37:58: 4000000 INFO @ Fri, 26 Jun 2020 23:38:03: 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 23:38:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.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 23:38:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:38:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:38:09: 6000000 INFO @ Fri, 26 Jun 2020 23:38:12: 1000000 INFO @ Fri, 26 Jun 2020 23:38:15: 7000000 INFO @ Fri, 26 Jun 2020 23:38:18: 2000000 INFO @ Fri, 26 Jun 2020 23:38:21: 8000000 INFO @ Fri, 26 Jun 2020 23:38:24: 3000000 INFO @ Fri, 26 Jun 2020 23:38:27: 9000000 INFO @ Fri, 26 Jun 2020 23:38:30: 4000000 INFO @ Fri, 26 Jun 2020 23:38:33: 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 23:38:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.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 23:38:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:38:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:38:36: 5000000 INFO @ Fri, 26 Jun 2020 23:38:39: 11000000 INFO @ Fri, 26 Jun 2020 23:38:42: 6000000 INFO @ Fri, 26 Jun 2020 23:38:42: 1000000 INFO @ Fri, 26 Jun 2020 23:38:46: 12000000 INFO @ Fri, 26 Jun 2020 23:38:48: 7000000 INFO @ Fri, 26 Jun 2020 23:38:49: 2000000 INFO @ Fri, 26 Jun 2020 23:38:52: 13000000 INFO @ Fri, 26 Jun 2020 23:38:55: 8000000 INFO @ Fri, 26 Jun 2020 23:38:55: 3000000 INFO @ Fri, 26 Jun 2020 23:38:59: 14000000 INFO @ Fri, 26 Jun 2020 23:39:01: 9000000 INFO @ Fri, 26 Jun 2020 23:39:01: 4000000 INFO @ Fri, 26 Jun 2020 23:39:05: 15000000 INFO @ Fri, 26 Jun 2020 23:39:08: 5000000 INFO @ Fri, 26 Jun 2020 23:39:08: 10000000 INFO @ Fri, 26 Jun 2020 23:39:12: 16000000 INFO @ Fri, 26 Jun 2020 23:39:14: 6000000 INFO @ Fri, 26 Jun 2020 23:39:15: 11000000 INFO @ Fri, 26 Jun 2020 23:39:19: 17000000 INFO @ Fri, 26 Jun 2020 23:39:21: 7000000 INFO @ Fri, 26 Jun 2020 23:39:22: 12000000 INFO @ Fri, 26 Jun 2020 23:39:25: 18000000 INFO @ Fri, 26 Jun 2020 23:39:28: 8000000 INFO @ Fri, 26 Jun 2020 23:39:29: 13000000 INFO @ Fri, 26 Jun 2020 23:39:32: 19000000 INFO @ Fri, 26 Jun 2020 23:39:34: 9000000 INFO @ Fri, 26 Jun 2020 23:39:36: 14000000 INFO @ Fri, 26 Jun 2020 23:39:39: 20000000 INFO @ Fri, 26 Jun 2020 23:39:41: 10000000 INFO @ Fri, 26 Jun 2020 23:39:43: 15000000 INFO @ Fri, 26 Jun 2020 23:39:45: 21000000 INFO @ Fri, 26 Jun 2020 23:39:47: 11000000 INFO @ Fri, 26 Jun 2020 23:39:49: 16000000 INFO @ Fri, 26 Jun 2020 23:39:52: 22000000 INFO @ Fri, 26 Jun 2020 23:39:54: 12000000 INFO @ Fri, 26 Jun 2020 23:39:56: 17000000 INFO @ Fri, 26 Jun 2020 23:39:59: 23000000 INFO @ Fri, 26 Jun 2020 23:40:01: 13000000 INFO @ Fri, 26 Jun 2020 23:40:03: 18000000 INFO @ Fri, 26 Jun 2020 23:40:06: 24000000 INFO @ Fri, 26 Jun 2020 23:40:08: 14000000 INFO @ Fri, 26 Jun 2020 23:40:10: 19000000 INFO @ Fri, 26 Jun 2020 23:40:12: 25000000 INFO @ Fri, 26 Jun 2020 23:40:14: 15000000 INFO @ Fri, 26 Jun 2020 23:40:16: 20000000 INFO @ Fri, 26 Jun 2020 23:40:19: 26000000 INFO @ Fri, 26 Jun 2020 23:40:21: 16000000 INFO @ Fri, 26 Jun 2020 23:40:23: 21000000 INFO @ Fri, 26 Jun 2020 23:40:25: 27000000 INFO @ Fri, 26 Jun 2020 23:40:27: 17000000 INFO @ Fri, 26 Jun 2020 23:40:30: 22000000 INFO @ Fri, 26 Jun 2020 23:40:32: 28000000 INFO @ Fri, 26 Jun 2020 23:40:34: 18000000 INFO @ Fri, 26 Jun 2020 23:40:37: 23000000 INFO @ Fri, 26 Jun 2020 23:40:38: 29000000 INFO @ Fri, 26 Jun 2020 23:40:40: 19000000 INFO @ Fri, 26 Jun 2020 23:40:43: 24000000 INFO @ Fri, 26 Jun 2020 23:40:45: 30000000 INFO @ Fri, 26 Jun 2020 23:40:47: 20000000 INFO @ Fri, 26 Jun 2020 23:40:50: 25000000 INFO @ Fri, 26 Jun 2020 23:40:52: 31000000 INFO @ Fri, 26 Jun 2020 23:40:54: 21000000 INFO @ Fri, 26 Jun 2020 23:40:58: 26000000 INFO @ Fri, 26 Jun 2020 23:40:59: 32000000 INFO @ Fri, 26 Jun 2020 23:41:01: 22000000 INFO @ Fri, 26 Jun 2020 23:41:05: 27000000 INFO @ Fri, 26 Jun 2020 23:41:06: 33000000 INFO @ Fri, 26 Jun 2020 23:41:08: 23000000 INFO @ Fri, 26 Jun 2020 23:41:13: 28000000 INFO @ Fri, 26 Jun 2020 23:41:13: 34000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:41:15: 24000000 INFO @ Fri, 26 Jun 2020 23:41:20: 35000000 INFO @ Fri, 26 Jun 2020 23:41:20: 29000000 INFO @ Fri, 26 Jun 2020 23:41:22: 25000000 INFO @ Fri, 26 Jun 2020 23:41:27: 36000000 INFO @ Fri, 26 Jun 2020 23:41:27: 30000000 INFO @ Fri, 26 Jun 2020 23:41:29: 26000000 INFO @ Fri, 26 Jun 2020 23:41:34: 37000000 INFO @ Fri, 26 Jun 2020 23:41:35: 31000000 INFO @ Fri, 26 Jun 2020 23:41:36: 27000000 INFO @ Fri, 26 Jun 2020 23:41:41: 38000000 INFO @ Fri, 26 Jun 2020 23:41:42: 32000000 INFO @ Fri, 26 Jun 2020 23:41:43: 28000000 INFO @ Fri, 26 Jun 2020 23:41:44: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:41:44: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:41:44: #1 total tags in treatment: 17525776 INFO @ Fri, 26 Jun 2020 23:41:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:41:44: #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 23:41:44: #1 tags after filtering in treatment: 15817458 INFO @ Fri, 26 Jun 2020 23:41:44: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 26 Jun 2020 23:41:44: #1 finished! INFO @ Fri, 26 Jun 2020 23:41:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:41:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:41:45: #2 number of paired peaks: 374 WARNING @ Fri, 26 Jun 2020 23:41:45: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Fri, 26 Jun 2020 23:41:45: start model_add_line... INFO @ Fri, 26 Jun 2020 23:41:46: start X-correlation... INFO @ Fri, 26 Jun 2020 23:41:46: end of X-cor INFO @ Fri, 26 Jun 2020 23:41:46: #2 finished! INFO @ Fri, 26 Jun 2020 23:41:46: #2 predicted fragment length is 114 bps INFO @ Fri, 26 Jun 2020 23:41:46: #2 alternative fragment length(s) may be 3,114 bps INFO @ Fri, 26 Jun 2020 23:41:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.05_model.r INFO @ Fri, 26 Jun 2020 23:41:46: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:41:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:41:50: 33000000 INFO @ Fri, 26 Jun 2020 23:41:50: 29000000 INFO @ Fri, 26 Jun 2020 23:41:57: 30000000 INFO @ Fri, 26 Jun 2020 23:41:57: 34000000 INFO @ Fri, 26 Jun 2020 23:42:04: 31000000 INFO @ Fri, 26 Jun 2020 23:42:05: 35000000 INFO @ Fri, 26 Jun 2020 23:42:11: 32000000 INFO @ Fri, 26 Jun 2020 23:42:13: 36000000 INFO @ Fri, 26 Jun 2020 23:42:18: 33000000 INFO @ Fri, 26 Jun 2020 23:42:19: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:42:20: 37000000 INFO @ Fri, 26 Jun 2020 23:42:25: 34000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:42:28: 38000000 INFO @ Fri, 26 Jun 2020 23:42:31: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:42:31: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:42:31: #1 total tags in treatment: 17525776 INFO @ Fri, 26 Jun 2020 23:42:31: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:42:31: #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 23:42:31: #1 tags after filtering in treatment: 15817458 INFO @ Fri, 26 Jun 2020 23:42:31: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 26 Jun 2020 23:42:31: #1 finished! INFO @ Fri, 26 Jun 2020 23:42:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:42:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:42:31: 35000000 INFO @ Fri, 26 Jun 2020 23:42:32: #2 number of paired peaks: 374 WARNING @ Fri, 26 Jun 2020 23:42:32: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Fri, 26 Jun 2020 23:42:32: start model_add_line... INFO @ Fri, 26 Jun 2020 23:42:32: start X-correlation... INFO @ Fri, 26 Jun 2020 23:42:32: end of X-cor INFO @ Fri, 26 Jun 2020 23:42:32: #2 finished! INFO @ Fri, 26 Jun 2020 23:42:32: #2 predicted fragment length is 114 bps INFO @ Fri, 26 Jun 2020 23:42:32: #2 alternative fragment length(s) may be 3,114 bps INFO @ Fri, 26 Jun 2020 23:42:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.10_model.r INFO @ Fri, 26 Jun 2020 23:42:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:42:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:42:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:42:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:42:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.05_summits.bed INFO @ Fri, 26 Jun 2020 23:42:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (519 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:42:37: 36000000 INFO @ Fri, 26 Jun 2020 23:42:43: 37000000 INFO @ Fri, 26 Jun 2020 23:42:49: 38000000 INFO @ Fri, 26 Jun 2020 23:42:51: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:42:51: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:42:51: #1 total tags in treatment: 17525776 INFO @ Fri, 26 Jun 2020 23:42:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:42:51: #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 23:42:52: #1 tags after filtering in treatment: 15817458 INFO @ Fri, 26 Jun 2020 23:42:52: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 26 Jun 2020 23:42:52: #1 finished! INFO @ Fri, 26 Jun 2020 23:42:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:42:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:42:53: #2 number of paired peaks: 374 WARNING @ Fri, 26 Jun 2020 23:42:53: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Fri, 26 Jun 2020 23:42:53: start model_add_line... INFO @ Fri, 26 Jun 2020 23:42:53: start X-correlation... INFO @ Fri, 26 Jun 2020 23:42:53: end of X-cor INFO @ Fri, 26 Jun 2020 23:42:53: #2 finished! INFO @ Fri, 26 Jun 2020 23:42:53: #2 predicted fragment length is 114 bps INFO @ Fri, 26 Jun 2020 23:42:53: #2 alternative fragment length(s) may be 3,114 bps INFO @ Fri, 26 Jun 2020 23:42:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.20_model.r INFO @ Fri, 26 Jun 2020 23:42:53: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:42:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:43:03: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:43:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:43:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:43:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.10_summits.bed INFO @ Fri, 26 Jun 2020 23:43:18: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (398 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:43:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:43:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:43:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:43:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1995058/SRX1995058.20_summits.bed INFO @ Fri, 26 Jun 2020 23:43:37: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (245 records, 4 fields): 2 millis CompletedMACS2peakCalling