Job ID = 6497377 SRX = SRX4085349 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T21:27:20 prefetch.2.10.7: 1) Downloading 'SRR7167378'... 2020-06-25T21:27:20 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:35:40 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:35:40 prefetch.2.10.7: 1) 'SRR7167378' was downloaded successfully Read 36867961 spots for SRR7167378/SRR7167378.sra Written 36867961 spots for SRR7167378/SRR7167378.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: 00:35:26 36867961 reads; of these: 36867961 (100.00%) were paired; of these: 6862692 (18.61%) aligned concordantly 0 times 26268470 (71.25%) aligned concordantly exactly 1 time 3736799 (10.14%) aligned concordantly >1 times ---- 6862692 pairs aligned concordantly 0 times; of these: 1279357 (18.64%) aligned discordantly 1 time ---- 5583335 pairs aligned 0 times concordantly or discordantly; of these: 11166670 mates make up the pairs; of these: 7531039 (67.44%) aligned 0 times 2759203 (24.71%) aligned exactly 1 time 876428 (7.85%) aligned >1 times 89.79% overall alignment rate Time searching: 00:35:26 Overall time: 00:35:26 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] 18210177 / 30259347 = 0.6018 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 07:31:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.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 07:31:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:31:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:31:20: 1000000 INFO @ Fri, 26 Jun 2020 07:31:25: 2000000 INFO @ Fri, 26 Jun 2020 07:31:30: 3000000 INFO @ Fri, 26 Jun 2020 07:31:36: 4000000 INFO @ Fri, 26 Jun 2020 07:31:41: 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 07:31:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.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 07:31:45: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:31:45: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:31:46: 6000000 INFO @ Fri, 26 Jun 2020 07:31:50: 1000000 INFO @ Fri, 26 Jun 2020 07:31:51: 7000000 INFO @ Fri, 26 Jun 2020 07:31:54: 2000000 INFO @ Fri, 26 Jun 2020 07:31:56: 8000000 INFO @ Fri, 26 Jun 2020 07:31:59: 3000000 INFO @ Fri, 26 Jun 2020 07:32:01: 9000000 INFO @ Fri, 26 Jun 2020 07:32:03: 4000000 INFO @ Fri, 26 Jun 2020 07:32:06: 10000000 INFO @ Fri, 26 Jun 2020 07:32:08: 5000000 INFO @ Fri, 26 Jun 2020 07:32:11: 11000000 INFO @ Fri, 26 Jun 2020 07:32:12: 6000000 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 07:32:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.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 07:32:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:32:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:32:17: 12000000 INFO @ Fri, 26 Jun 2020 07:32:17: 7000000 INFO @ Fri, 26 Jun 2020 07:32:20: 1000000 INFO @ Fri, 26 Jun 2020 07:32:22: 8000000 INFO @ Fri, 26 Jun 2020 07:32:22: 13000000 INFO @ Fri, 26 Jun 2020 07:32:26: 2000000 INFO @ Fri, 26 Jun 2020 07:32:26: 9000000 INFO @ Fri, 26 Jun 2020 07:32:27: 14000000 INFO @ Fri, 26 Jun 2020 07:32:31: 10000000 INFO @ Fri, 26 Jun 2020 07:32:31: 3000000 INFO @ Fri, 26 Jun 2020 07:32:33: 15000000 INFO @ Fri, 26 Jun 2020 07:32:35: 11000000 INFO @ Fri, 26 Jun 2020 07:32:37: 4000000 INFO @ Fri, 26 Jun 2020 07:32:38: 16000000 INFO @ Fri, 26 Jun 2020 07:32:40: 12000000 INFO @ Fri, 26 Jun 2020 07:32:42: 5000000 INFO @ Fri, 26 Jun 2020 07:32:43: 17000000 INFO @ Fri, 26 Jun 2020 07:32:44: 13000000 INFO @ Fri, 26 Jun 2020 07:32:48: 6000000 INFO @ Fri, 26 Jun 2020 07:32:49: 18000000 INFO @ Fri, 26 Jun 2020 07:32:49: 14000000 INFO @ Fri, 26 Jun 2020 07:32:53: 15000000 INFO @ Fri, 26 Jun 2020 07:32:53: 7000000 INFO @ Fri, 26 Jun 2020 07:32:54: 19000000 INFO @ Fri, 26 Jun 2020 07:32:58: 16000000 INFO @ Fri, 26 Jun 2020 07:32:59: 8000000 INFO @ Fri, 26 Jun 2020 07:32:59: 20000000 INFO @ Fri, 26 Jun 2020 07:33:02: 17000000 INFO @ Fri, 26 Jun 2020 07:33:04: 21000000 INFO @ Fri, 26 Jun 2020 07:33:04: 9000000 INFO @ Fri, 26 Jun 2020 07:33:07: 18000000 INFO @ Fri, 26 Jun 2020 07:33:09: 22000000 INFO @ Fri, 26 Jun 2020 07:33:10: 10000000 INFO @ Fri, 26 Jun 2020 07:33:11: 19000000 INFO @ Fri, 26 Jun 2020 07:33:14: 23000000 INFO @ Fri, 26 Jun 2020 07:33:15: 11000000 INFO @ Fri, 26 Jun 2020 07:33:16: 20000000 INFO @ Fri, 26 Jun 2020 07:33:19: 24000000 INFO @ Fri, 26 Jun 2020 07:33:20: 12000000 INFO @ Fri, 26 Jun 2020 07:33:20: 21000000 INFO @ Fri, 26 Jun 2020 07:33:24: 25000000 INFO @ Fri, 26 Jun 2020 07:33:25: 22000000 INFO @ Fri, 26 Jun 2020 07:33:25: 13000000 INFO @ Fri, 26 Jun 2020 07:33:29: 23000000 INFO @ Fri, 26 Jun 2020 07:33:29: 26000000 INFO @ Fri, 26 Jun 2020 07:33:31: 14000000 INFO @ Fri, 26 Jun 2020 07:33:34: 24000000 INFO @ Fri, 26 Jun 2020 07:33:35: 27000000 INFO @ Fri, 26 Jun 2020 07:33:36: 15000000 INFO @ Fri, 26 Jun 2020 07:33:38: 25000000 INFO @ Fri, 26 Jun 2020 07:33:40: 28000000 INFO @ Fri, 26 Jun 2020 07:33:41: 16000000 INFO @ Fri, 26 Jun 2020 07:33:43: 26000000 INFO @ Fri, 26 Jun 2020 07:33:45: 29000000 INFO @ Fri, 26 Jun 2020 07:33:47: 17000000 INFO @ Fri, 26 Jun 2020 07:33:47: 27000000 INFO @ Fri, 26 Jun 2020 07:33:48: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:33:48: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:33:48: #1 total tags in treatment: 11927399 INFO @ Fri, 26 Jun 2020 07:33:48: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:33:48: #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 07:33:49: #1 tags after filtering in treatment: 10069135 INFO @ Fri, 26 Jun 2020 07:33:49: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 26 Jun 2020 07:33:49: #1 finished! INFO @ Fri, 26 Jun 2020 07:33:49: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:33:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:33:49: #2 number of paired peaks: 451 WARNING @ Fri, 26 Jun 2020 07:33:49: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Fri, 26 Jun 2020 07:33:49: start model_add_line... INFO @ Fri, 26 Jun 2020 07:33:49: start X-correlation... INFO @ Fri, 26 Jun 2020 07:33:49: end of X-cor INFO @ Fri, 26 Jun 2020 07:33:49: #2 finished! INFO @ Fri, 26 Jun 2020 07:33:49: #2 predicted fragment length is 111 bps INFO @ Fri, 26 Jun 2020 07:33:49: #2 alternative fragment length(s) may be 111 bps INFO @ Fri, 26 Jun 2020 07:33:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.05_model.r INFO @ Fri, 26 Jun 2020 07:33:49: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:33:49: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:33:51: 28000000 INFO @ Fri, 26 Jun 2020 07:33:52: 18000000 INFO @ Fri, 26 Jun 2020 07:33:56: 29000000 INFO @ Fri, 26 Jun 2020 07:33:57: 19000000 INFO @ Fri, 26 Jun 2020 07:33:59: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:33:59: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:33:59: #1 total tags in treatment: 11927399 INFO @ Fri, 26 Jun 2020 07:33:59: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:33:59: #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 07:33:59: #1 tags after filtering in treatment: 10069135 INFO @ Fri, 26 Jun 2020 07:33:59: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 26 Jun 2020 07:33:59: #1 finished! INFO @ Fri, 26 Jun 2020 07:33:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:33:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:34:00: #2 number of paired peaks: 451 WARNING @ Fri, 26 Jun 2020 07:34:00: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Fri, 26 Jun 2020 07:34:00: start model_add_line... INFO @ Fri, 26 Jun 2020 07:34:00: start X-correlation... INFO @ Fri, 26 Jun 2020 07:34:00: end of X-cor INFO @ Fri, 26 Jun 2020 07:34:00: #2 finished! INFO @ Fri, 26 Jun 2020 07:34:00: #2 predicted fragment length is 111 bps INFO @ Fri, 26 Jun 2020 07:34:00: #2 alternative fragment length(s) may be 111 bps INFO @ Fri, 26 Jun 2020 07:34:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.10_model.r INFO @ Fri, 26 Jun 2020 07:34:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:34:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:34:02: 20000000 INFO @ Fri, 26 Jun 2020 07:34:07: 21000000 INFO @ Fri, 26 Jun 2020 07:34:10: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:34:12: 22000000 INFO @ Fri, 26 Jun 2020 07:34:18: 23000000 INFO @ Fri, 26 Jun 2020 07:34:19: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:34:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:34:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:34:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.05_summits.bed INFO @ Fri, 26 Jun 2020 07:34:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2083 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:34:23: 24000000 INFO @ Fri, 26 Jun 2020 07:34:28: 25000000 INFO @ Fri, 26 Jun 2020 07:34:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:34:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:34:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.10_summits.bed INFO @ Fri, 26 Jun 2020 07:34:29: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1247 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:34:33: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:34:38: 27000000 INFO @ Fri, 26 Jun 2020 07:34:43: 28000000 INFO @ Fri, 26 Jun 2020 07:34:48: 29000000 INFO @ Fri, 26 Jun 2020 07:34:51: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:34:51: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:34:51: #1 total tags in treatment: 11927399 INFO @ Fri, 26 Jun 2020 07:34:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:34:51: #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 07:34:52: #1 tags after filtering in treatment: 10069135 INFO @ Fri, 26 Jun 2020 07:34:52: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 26 Jun 2020 07:34:52: #1 finished! INFO @ Fri, 26 Jun 2020 07:34:52: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:34:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:34:52: #2 number of paired peaks: 451 WARNING @ Fri, 26 Jun 2020 07:34:52: Fewer paired peaks (451) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 451 pairs to build model! INFO @ Fri, 26 Jun 2020 07:34:52: start model_add_line... INFO @ Fri, 26 Jun 2020 07:34:52: start X-correlation... INFO @ Fri, 26 Jun 2020 07:34:52: end of X-cor INFO @ Fri, 26 Jun 2020 07:34:52: #2 finished! INFO @ Fri, 26 Jun 2020 07:34:52: #2 predicted fragment length is 111 bps INFO @ Fri, 26 Jun 2020 07:34:52: #2 alternative fragment length(s) may be 111 bps INFO @ Fri, 26 Jun 2020 07:34:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.20_model.r INFO @ Fri, 26 Jun 2020 07:34:52: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:34:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:35:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:35:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:35:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:35:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085349/SRX4085349.20_summits.bed INFO @ Fri, 26 Jun 2020 07:35:22: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (703 records, 4 fields): 2 millis CompletedMACS2peakCalling