Job ID = 6497394 SRX = SRX4085428 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T21:16:04 prefetch.2.10.7: 1) Downloading 'SRR7167457'... 2020-06-25T21:16:04 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:22:14 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:22:14 prefetch.2.10.7: 1) 'SRR7167457' was downloaded successfully Read 22413526 spots for SRR7167457/SRR7167457.sra Written 22413526 spots for SRR7167457/SRR7167457.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: 00:19:51 22413526 reads; of these: 22413526 (100.00%) were paired; of these: 1270013 (5.67%) aligned concordantly 0 times 18365848 (81.94%) aligned concordantly exactly 1 time 2777665 (12.39%) aligned concordantly >1 times ---- 1270013 pairs aligned concordantly 0 times; of these: 616266 (48.52%) aligned discordantly 1 time ---- 653747 pairs aligned 0 times concordantly or discordantly; of these: 1307494 mates make up the pairs; of these: 531524 (40.65%) aligned 0 times 452466 (34.61%) aligned exactly 1 time 323504 (24.74%) aligned >1 times 98.81% overall alignment rate Time searching: 00:19:51 Overall time: 00:19:51 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 20 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] 8226220 / 21270228 = 0.3867 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 07:01:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.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 07:01:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:01:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:01:19: 1000000 INFO @ Fri, 26 Jun 2020 07:01:25: 2000000 INFO @ Fri, 26 Jun 2020 07:01:32: 3000000 INFO @ Fri, 26 Jun 2020 07:01:38: 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 07:01:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.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 07:01:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:01:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:01:44: 5000000 INFO @ Fri, 26 Jun 2020 07:01:49: 1000000 INFO @ Fri, 26 Jun 2020 07:01:51: 6000000 INFO @ Fri, 26 Jun 2020 07:01:56: 2000000 INFO @ Fri, 26 Jun 2020 07:01:57: 7000000 INFO @ Fri, 26 Jun 2020 07:02:02: 3000000 INFO @ Fri, 26 Jun 2020 07:02:04: 8000000 INFO @ Fri, 26 Jun 2020 07:02:08: 4000000 INFO @ Fri, 26 Jun 2020 07:02:10: 9000000 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 07:02:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.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 07:02:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:02:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:02:15: 5000000 INFO @ Fri, 26 Jun 2020 07:02:17: 10000000 INFO @ Fri, 26 Jun 2020 07:02:20: 1000000 INFO @ Fri, 26 Jun 2020 07:02:21: 6000000 INFO @ Fri, 26 Jun 2020 07:02:23: 11000000 INFO @ Fri, 26 Jun 2020 07:02:26: 2000000 INFO @ Fri, 26 Jun 2020 07:02:28: 7000000 INFO @ Fri, 26 Jun 2020 07:02:30: 12000000 INFO @ Fri, 26 Jun 2020 07:02:33: 3000000 INFO @ Fri, 26 Jun 2020 07:02:34: 8000000 INFO @ Fri, 26 Jun 2020 07:02:37: 13000000 INFO @ Fri, 26 Jun 2020 07:02:40: 4000000 INFO @ Fri, 26 Jun 2020 07:02:41: 9000000 INFO @ Fri, 26 Jun 2020 07:02:44: 14000000 INFO @ Fri, 26 Jun 2020 07:02:46: 5000000 INFO @ Fri, 26 Jun 2020 07:02:47: 10000000 INFO @ Fri, 26 Jun 2020 07:02:50: 15000000 INFO @ Fri, 26 Jun 2020 07:02:53: 6000000 INFO @ Fri, 26 Jun 2020 07:02:54: 11000000 INFO @ Fri, 26 Jun 2020 07:02:57: 16000000 INFO @ Fri, 26 Jun 2020 07:03:00: 7000000 INFO @ Fri, 26 Jun 2020 07:03:00: 12000000 INFO @ Fri, 26 Jun 2020 07:03:03: 17000000 INFO @ Fri, 26 Jun 2020 07:03:06: 8000000 INFO @ Fri, 26 Jun 2020 07:03:07: 13000000 INFO @ Fri, 26 Jun 2020 07:03:10: 18000000 INFO @ Fri, 26 Jun 2020 07:03:12: 9000000 INFO @ Fri, 26 Jun 2020 07:03:13: 14000000 INFO @ Fri, 26 Jun 2020 07:03:16: 19000000 INFO @ Fri, 26 Jun 2020 07:03:19: 10000000 INFO @ Fri, 26 Jun 2020 07:03:20: 15000000 INFO @ Fri, 26 Jun 2020 07:03:22: 20000000 INFO @ Fri, 26 Jun 2020 07:03:25: 11000000 INFO @ Fri, 26 Jun 2020 07:03:26: 16000000 INFO @ Fri, 26 Jun 2020 07:03:29: 21000000 INFO @ Fri, 26 Jun 2020 07:03:32: 12000000 INFO @ Fri, 26 Jun 2020 07:03:33: 17000000 INFO @ Fri, 26 Jun 2020 07:03:35: 22000000 INFO @ Fri, 26 Jun 2020 07:03:39: 13000000 INFO @ Fri, 26 Jun 2020 07:03:39: 18000000 INFO @ Fri, 26 Jun 2020 07:03:41: 23000000 INFO @ Fri, 26 Jun 2020 07:03:46: 14000000 INFO @ Fri, 26 Jun 2020 07:03:46: 19000000 INFO @ Fri, 26 Jun 2020 07:03:48: 24000000 INFO @ Fri, 26 Jun 2020 07:03:53: 20000000 INFO @ Fri, 26 Jun 2020 07:03:54: 15000000 INFO @ Fri, 26 Jun 2020 07:03:56: 25000000 INFO @ Fri, 26 Jun 2020 07:04:00: 21000000 INFO @ Fri, 26 Jun 2020 07:04:02: 16000000 INFO @ Fri, 26 Jun 2020 07:04:02: 26000000 INFO @ Fri, 26 Jun 2020 07:04:06: 22000000 INFO @ Fri, 26 Jun 2020 07:04:09: 27000000 INFO @ Fri, 26 Jun 2020 07:04:09: 17000000 INFO @ Fri, 26 Jun 2020 07:04:12: 23000000 INFO @ Fri, 26 Jun 2020 07:04:14: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:04:14: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:04:14: #1 total tags in treatment: 12961405 INFO @ Fri, 26 Jun 2020 07:04:14: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:04:14: #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 07:04:14: #1 tags after filtering in treatment: 10734172 INFO @ Fri, 26 Jun 2020 07:04:14: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 26 Jun 2020 07:04:14: #1 finished! INFO @ Fri, 26 Jun 2020 07:04:14: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:04:14: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:04:15: #2 number of paired peaks: 281 WARNING @ Fri, 26 Jun 2020 07:04:15: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Fri, 26 Jun 2020 07:04:15: start model_add_line... INFO @ Fri, 26 Jun 2020 07:04:15: start X-correlation... INFO @ Fri, 26 Jun 2020 07:04:15: end of X-cor INFO @ Fri, 26 Jun 2020 07:04:15: #2 finished! INFO @ Fri, 26 Jun 2020 07:04:15: #2 predicted fragment length is 128 bps INFO @ Fri, 26 Jun 2020 07:04:15: #2 alternative fragment length(s) may be 4,128 bps INFO @ Fri, 26 Jun 2020 07:04:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.05_model.r INFO @ Fri, 26 Jun 2020 07:04:16: 18000000 INFO @ Fri, 26 Jun 2020 07:04:18: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:04:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:04:18: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:04:23: 19000000 INFO @ Fri, 26 Jun 2020 07:04:25: 25000000 INFO @ Fri, 26 Jun 2020 07:04:29: 20000000 INFO @ Fri, 26 Jun 2020 07:04:31: 26000000 INFO @ Fri, 26 Jun 2020 07:04:35: 21000000 INFO @ Fri, 26 Jun 2020 07:04:37: 27000000 INFO @ Fri, 26 Jun 2020 07:04:41: 22000000 INFO @ Fri, 26 Jun 2020 07:04:42: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:04:42: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:04:42: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:04:42: #1 total tags in treatment: 12961405 INFO @ Fri, 26 Jun 2020 07:04:42: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:04:42: #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 07:04:42: #1 tags after filtering in treatment: 10734172 INFO @ Fri, 26 Jun 2020 07:04:42: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 26 Jun 2020 07:04:42: #1 finished! INFO @ Fri, 26 Jun 2020 07:04:42: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:04:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:04:43: #2 number of paired peaks: 281 WARNING @ Fri, 26 Jun 2020 07:04:43: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Fri, 26 Jun 2020 07:04:43: start model_add_line... INFO @ Fri, 26 Jun 2020 07:04:43: start X-correlation... INFO @ Fri, 26 Jun 2020 07:04:43: end of X-cor INFO @ Fri, 26 Jun 2020 07:04:43: #2 finished! INFO @ Fri, 26 Jun 2020 07:04:43: #2 predicted fragment length is 128 bps INFO @ Fri, 26 Jun 2020 07:04:43: #2 alternative fragment length(s) may be 4,128 bps INFO @ Fri, 26 Jun 2020 07:04:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.10_model.r INFO @ Fri, 26 Jun 2020 07:04:43: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:04:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:04:47: 23000000 INFO @ Fri, 26 Jun 2020 07:04:53: 24000000 INFO @ Fri, 26 Jun 2020 07:04:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:04:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:04:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.05_summits.bed INFO @ Fri, 26 Jun 2020 07:04:54: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1782 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:05:00: 25000000 INFO @ Fri, 26 Jun 2020 07:05:06: 26000000 INFO @ Fri, 26 Jun 2020 07:05:07: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:05:13: 27000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:05:18: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:05:18: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:05:18: #1 total tags in treatment: 12961405 INFO @ Fri, 26 Jun 2020 07:05:18: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:05:18: #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 07:05:19: #1 tags after filtering in treatment: 10734172 INFO @ Fri, 26 Jun 2020 07:05:19: #1 Redundant rate of treatment: 0.17 INFO @ Fri, 26 Jun 2020 07:05:19: #1 finished! INFO @ Fri, 26 Jun 2020 07:05:19: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:05:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:05:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:05:19: #2 number of paired peaks: 281 WARNING @ Fri, 26 Jun 2020 07:05:19: Fewer paired peaks (281) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 281 pairs to build model! INFO @ Fri, 26 Jun 2020 07:05:19: start model_add_line... INFO @ Fri, 26 Jun 2020 07:05:19: start X-correlation... INFO @ Fri, 26 Jun 2020 07:05:19: end of X-cor INFO @ Fri, 26 Jun 2020 07:05:19: #2 finished! INFO @ Fri, 26 Jun 2020 07:05:19: #2 predicted fragment length is 128 bps INFO @ Fri, 26 Jun 2020 07:05:19: #2 alternative fragment length(s) may be 4,128 bps INFO @ Fri, 26 Jun 2020 07:05:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.20_model.r INFO @ Fri, 26 Jun 2020 07:05:42: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:05:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:05:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:05:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.10_summits.bed INFO @ Fri, 26 Jun 2020 07:05:42: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (811 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:06:05: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:06:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:06:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:06:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085428/SRX4085428.20_summits.bed INFO @ Fri, 26 Jun 2020 07:06:47: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (327 records, 4 fields): 2 millis CompletedMACS2peakCalling