Job ID = 6497350 SRX = SRX1995058 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T21:48:18 prefetch.2.10.7: 1) Downloading 'SRR3993990'... 2020-06-25T21:48:40 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:53:56 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:53:56 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:31:51 33075103 reads; of these: 33075103 (100.00%) were paired; of these: 3887374 (11.75%) aligned concordantly 0 times 25134093 (75.99%) aligned concordantly exactly 1 time 4053636 (12.26%) aligned concordantly >1 times ---- 3887374 pairs aligned concordantly 0 times; of these: 944636 (24.30%) aligned discordantly 1 time ---- 2942738 pairs aligned 0 times concordantly or discordantly; of these: 5885476 mates make up the pairs; of these: 3941620 (66.97%) aligned 0 times 1410003 (23.96%) aligned exactly 1 time 533853 (9.07%) aligned >1 times 94.04% overall alignment rate Time searching: 00:31:55 Overall time: 00:31:56 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] 11914825 / 30087091 = 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 07:43:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1995058/SRX1995058.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1995058/SRX1995058.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1995058/SRX1995058.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:43:21: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:43:21: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:43:27: 1000000 INFO @ Fri, 26 Jun 2020 07:43:32: 2000000 INFO @ Fri, 26 Jun 2020 07:43:38: 3000000 INFO @ Fri, 26 Jun 2020 07:43:43: 4000000 INFO @ Fri, 26 Jun 2020 07:43:49: 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 07:43:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1995058/SRX1995058.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1995058/SRX1995058.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1995058/SRX1995058.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:43:51: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:43:51: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:43:55: 6000000 INFO @ Fri, 26 Jun 2020 07:43:58: 1000000 INFO @ Fri, 26 Jun 2020 07:44:01: 7000000 INFO @ Fri, 26 Jun 2020 07:44:04: 2000000 INFO @ Fri, 26 Jun 2020 07:44:07: 8000000 INFO @ Fri, 26 Jun 2020 07:44:10: 3000000 INFO @ Fri, 26 Jun 2020 07:44:14: 9000000 INFO @ Fri, 26 Jun 2020 07:44:16: 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 @ Fri, 26 Jun 2020 07:44:20: 10000000 INFO @ Fri, 26 Jun 2020 07:44:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1995058/SRX1995058.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1995058/SRX1995058.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1995058/SRX1995058.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:44:22: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:44:22: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:44:23: 5000000 INFO @ Fri, 26 Jun 2020 07:44:26: 11000000 INFO @ Fri, 26 Jun 2020 07:44:28: 1000000 INFO @ Fri, 26 Jun 2020 07:44:29: 6000000 INFO @ Fri, 26 Jun 2020 07:44:33: 12000000 INFO @ Fri, 26 Jun 2020 07:44:35: 2000000 INFO @ Fri, 26 Jun 2020 07:44:35: 7000000 INFO @ Fri, 26 Jun 2020 07:44:40: 13000000 INFO @ Fri, 26 Jun 2020 07:44:41: 3000000 INFO @ Fri, 26 Jun 2020 07:44:42: 8000000 INFO @ Fri, 26 Jun 2020 07:44:46: 14000000 INFO @ Fri, 26 Jun 2020 07:44:48: 4000000 INFO @ Fri, 26 Jun 2020 07:44:48: 9000000 INFO @ Fri, 26 Jun 2020 07:44:53: 15000000 INFO @ Fri, 26 Jun 2020 07:44:54: 10000000 INFO @ Fri, 26 Jun 2020 07:44:54: 5000000 INFO @ Fri, 26 Jun 2020 07:44:59: 16000000 INFO @ Fri, 26 Jun 2020 07:45:00: 11000000 INFO @ Fri, 26 Jun 2020 07:45:01: 6000000 INFO @ Fri, 26 Jun 2020 07:45:06: 17000000 INFO @ Fri, 26 Jun 2020 07:45:07: 12000000 INFO @ Fri, 26 Jun 2020 07:45:07: 7000000 INFO @ Fri, 26 Jun 2020 07:45:12: 18000000 INFO @ Fri, 26 Jun 2020 07:45:13: 13000000 INFO @ Fri, 26 Jun 2020 07:45:14: 8000000 INFO @ Fri, 26 Jun 2020 07:45:18: 19000000 INFO @ Fri, 26 Jun 2020 07:45:19: 14000000 INFO @ Fri, 26 Jun 2020 07:45:20: 9000000 INFO @ Fri, 26 Jun 2020 07:45:25: 20000000 INFO @ Fri, 26 Jun 2020 07:45:26: 15000000 INFO @ Fri, 26 Jun 2020 07:45:26: 10000000 INFO @ Fri, 26 Jun 2020 07:45:31: 21000000 INFO @ Fri, 26 Jun 2020 07:45:32: 16000000 INFO @ Fri, 26 Jun 2020 07:45:33: 11000000 INFO @ Fri, 26 Jun 2020 07:45:38: 22000000 INFO @ Fri, 26 Jun 2020 07:45:38: 17000000 INFO @ Fri, 26 Jun 2020 07:45:39: 12000000 INFO @ Fri, 26 Jun 2020 07:45:44: 23000000 INFO @ Fri, 26 Jun 2020 07:45:44: 18000000 INFO @ Fri, 26 Jun 2020 07:45:46: 13000000 INFO @ Fri, 26 Jun 2020 07:45:50: 19000000 INFO @ Fri, 26 Jun 2020 07:45:50: 24000000 INFO @ Fri, 26 Jun 2020 07:45:52: 14000000 INFO @ Fri, 26 Jun 2020 07:45:56: 20000000 INFO @ Fri, 26 Jun 2020 07:45:57: 25000000 INFO @ Fri, 26 Jun 2020 07:45:58: 15000000 INFO @ Fri, 26 Jun 2020 07:46:03: 21000000 INFO @ Fri, 26 Jun 2020 07:46:03: 26000000 INFO @ Fri, 26 Jun 2020 07:46:05: 16000000 INFO @ Fri, 26 Jun 2020 07:46:09: 22000000 INFO @ Fri, 26 Jun 2020 07:46:09: 27000000 INFO @ Fri, 26 Jun 2020 07:46:11: 17000000 INFO @ Fri, 26 Jun 2020 07:46:15: 23000000 INFO @ Fri, 26 Jun 2020 07:46:16: 28000000 INFO @ Fri, 26 Jun 2020 07:46:17: 18000000 INFO @ Fri, 26 Jun 2020 07:46:21: 24000000 INFO @ Fri, 26 Jun 2020 07:46:22: 29000000 INFO @ Fri, 26 Jun 2020 07:46:23: 19000000 INFO @ Fri, 26 Jun 2020 07:46:27: 25000000 INFO @ Fri, 26 Jun 2020 07:46:28: 30000000 INFO @ Fri, 26 Jun 2020 07:46:30: 20000000 INFO @ Fri, 26 Jun 2020 07:46:33: 26000000 INFO @ Fri, 26 Jun 2020 07:46:34: 31000000 INFO @ Fri, 26 Jun 2020 07:46:36: 21000000 INFO @ Fri, 26 Jun 2020 07:46:39: 27000000 INFO @ Fri, 26 Jun 2020 07:46:40: 32000000 INFO @ Fri, 26 Jun 2020 07:46:42: 22000000 INFO @ Fri, 26 Jun 2020 07:46:45: 28000000 INFO @ Fri, 26 Jun 2020 07:46:47: 33000000 INFO @ Fri, 26 Jun 2020 07:46:48: 23000000 INFO @ Fri, 26 Jun 2020 07:46:51: 29000000 INFO @ Fri, 26 Jun 2020 07:46:53: 34000000 INFO @ Fri, 26 Jun 2020 07:46:54: 24000000 INFO @ Fri, 26 Jun 2020 07:46:57: 30000000 INFO @ Fri, 26 Jun 2020 07:46:59: 35000000 INFO @ Fri, 26 Jun 2020 07:47:00: 25000000 INFO @ Fri, 26 Jun 2020 07:47:03: 31000000 INFO @ Fri, 26 Jun 2020 07:47:05: 36000000 INFO @ Fri, 26 Jun 2020 07:47:06: 26000000 INFO @ Fri, 26 Jun 2020 07:47:09: 32000000 INFO @ Fri, 26 Jun 2020 07:47:11: 37000000 INFO @ Fri, 26 Jun 2020 07:47:12: 27000000 INFO @ Fri, 26 Jun 2020 07:47:15: 33000000 INFO @ Fri, 26 Jun 2020 07:47:17: 38000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:47:18: 28000000 INFO @ Fri, 26 Jun 2020 07:47:19: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:47:19: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:47:19: #1 total tags in treatment: 17525698 INFO @ Fri, 26 Jun 2020 07:47:19: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:47:19: #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 07:47:19: #1 tags after filtering in treatment: 15817383 INFO @ Fri, 26 Jun 2020 07:47:19: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 26 Jun 2020 07:47:19: #1 finished! INFO @ Fri, 26 Jun 2020 07:47:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:47:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:47:20: #2 number of paired peaks: 373 WARNING @ Fri, 26 Jun 2020 07:47:20: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Fri, 26 Jun 2020 07:47:20: start model_add_line... INFO @ Fri, 26 Jun 2020 07:47:20: start X-correlation... INFO @ Fri, 26 Jun 2020 07:47:20: end of X-cor INFO @ Fri, 26 Jun 2020 07:47:20: #2 finished! INFO @ Fri, 26 Jun 2020 07:47:20: #2 predicted fragment length is 114 bps INFO @ Fri, 26 Jun 2020 07:47:20: #2 alternative fragment length(s) may be 3,114 bps INFO @ Fri, 26 Jun 2020 07:47:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1995058/SRX1995058.05_model.r INFO @ Fri, 26 Jun 2020 07:47:20: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:47:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:47:21: 34000000 INFO @ Fri, 26 Jun 2020 07:47:24: 29000000 INFO @ Fri, 26 Jun 2020 07:47:27: 35000000 INFO @ Fri, 26 Jun 2020 07:47:30: 30000000 INFO @ Fri, 26 Jun 2020 07:47:33: 36000000 INFO @ Fri, 26 Jun 2020 07:47:36: 31000000 INFO @ Fri, 26 Jun 2020 07:47:39: 37000000 INFO @ Fri, 26 Jun 2020 07:47:42: 32000000 INFO @ Fri, 26 Jun 2020 07:47:45: 38000000 INFO @ Fri, 26 Jun 2020 07:47:47: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:47:47: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:47:47: #1 total tags in treatment: 17525698 INFO @ Fri, 26 Jun 2020 07:47:47: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:47:47: #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 07:47:47: #1 tags after filtering in treatment: 15817383 INFO @ Fri, 26 Jun 2020 07:47:47: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 26 Jun 2020 07:47:47: #1 finished! INFO @ Fri, 26 Jun 2020 07:47:47: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:47:47: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:47:48: 33000000 INFO @ Fri, 26 Jun 2020 07:47:48: #2 number of paired peaks: 373 WARNING @ Fri, 26 Jun 2020 07:47:48: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Fri, 26 Jun 2020 07:47:48: start model_add_line... INFO @ Fri, 26 Jun 2020 07:47:48: start X-correlation... INFO @ Fri, 26 Jun 2020 07:47:48: end of X-cor INFO @ Fri, 26 Jun 2020 07:47:48: #2 finished! INFO @ Fri, 26 Jun 2020 07:47:48: #2 predicted fragment length is 114 bps INFO @ Fri, 26 Jun 2020 07:47:48: #2 alternative fragment length(s) may be 3,114 bps INFO @ Fri, 26 Jun 2020 07:47:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1995058/SRX1995058.10_model.r INFO @ Fri, 26 Jun 2020 07:47:48: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:47:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:47:49: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:47:53: 34000000 INFO @ Fri, 26 Jun 2020 07:47:58: 35000000 INFO @ Fri, 26 Jun 2020 07:48:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1995058/SRX1995058.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:48:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1995058/SRX1995058.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:48:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1995058/SRX1995058.05_summits.bed INFO @ Fri, 26 Jun 2020 07:48:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (519 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:48:03: 36000000 INFO @ Fri, 26 Jun 2020 07:48:08: 37000000 INFO @ Fri, 26 Jun 2020 07:48:13: 38000000 INFO @ Fri, 26 Jun 2020 07:48:15: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:48:15: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:48:15: #1 total tags in treatment: 17525698 INFO @ Fri, 26 Jun 2020 07:48:15: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:48:15: #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 07:48:15: #1 tags after filtering in treatment: 15817383 INFO @ Fri, 26 Jun 2020 07:48:15: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 26 Jun 2020 07:48:15: #1 finished! INFO @ Fri, 26 Jun 2020 07:48:15: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:48:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:48:16: #2 number of paired peaks: 373 WARNING @ Fri, 26 Jun 2020 07:48:16: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Fri, 26 Jun 2020 07:48:16: start model_add_line... INFO @ Fri, 26 Jun 2020 07:48:16: start X-correlation... INFO @ Fri, 26 Jun 2020 07:48:16: end of X-cor INFO @ Fri, 26 Jun 2020 07:48:16: #2 finished! INFO @ Fri, 26 Jun 2020 07:48:16: #2 predicted fragment length is 114 bps INFO @ Fri, 26 Jun 2020 07:48:16: #2 alternative fragment length(s) may be 3,114 bps INFO @ Fri, 26 Jun 2020 07:48:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1995058/SRX1995058.20_model.r INFO @ Fri, 26 Jun 2020 07:48:16: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:48:16: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:48:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:48:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1995058/SRX1995058.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:48:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1995058/SRX1995058.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:48:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1995058/SRX1995058.10_summits.bed INFO @ Fri, 26 Jun 2020 07:48:30: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (397 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:48:44: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:48:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1995058/SRX1995058.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:48:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1995058/SRX1995058.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:48:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1995058/SRX1995058.20_summits.bed INFO @ Fri, 26 Jun 2020 07:48:58: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (245 records, 4 fields): 10 millis CompletedMACS2peakCalling