Job ID = 6497378 SRX = SRX4085354 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T21:56:41 prefetch.2.10.7: 1) Downloading 'SRR7167383'... 2020-06-25T21:56:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:04:45 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:04:45 prefetch.2.10.7: 1) 'SRR7167383' was downloaded successfully Read 40640884 spots for SRR7167383/SRR7167383.sra Written 40640884 spots for SRR7167383/SRR7167383.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: 00:00:01 Multiseed full-index search: 00:32:15 40640884 reads; of these: 40640884 (100.00%) were paired; of these: 3658097 (9.00%) aligned concordantly 0 times 32896777 (80.95%) aligned concordantly exactly 1 time 4086010 (10.05%) aligned concordantly >1 times ---- 3658097 pairs aligned concordantly 0 times; of these: 496563 (13.57%) aligned discordantly 1 time ---- 3161534 pairs aligned 0 times concordantly or discordantly; of these: 6323068 mates make up the pairs; of these: 4216624 (66.69%) aligned 0 times 1658786 (26.23%) aligned exactly 1 time 447658 (7.08%) aligned >1 times 94.81% overall alignment rate Time searching: 00:32:16 Overall time: 00:32:16 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 32 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] 23983515 / 37264131 = 0.6436 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 08:01:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.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 08:01:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:01:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:01:18: 1000000 INFO @ Fri, 26 Jun 2020 08:01:24: 2000000 INFO @ Fri, 26 Jun 2020 08:01:30: 3000000 INFO @ Fri, 26 Jun 2020 08:01:37: 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 08:01:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.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 08:01:42: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:01:42: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:01:43: 5000000 INFO @ Fri, 26 Jun 2020 08:01:48: 1000000 INFO @ Fri, 26 Jun 2020 08:01:49: 6000000 INFO @ Fri, 26 Jun 2020 08:01:54: 2000000 INFO @ Fri, 26 Jun 2020 08:01:56: 7000000 INFO @ Fri, 26 Jun 2020 08:02:01: 3000000 INFO @ Fri, 26 Jun 2020 08:02:02: 8000000 INFO @ Fri, 26 Jun 2020 08:02:07: 4000000 INFO @ Fri, 26 Jun 2020 08:02:09: 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 08:02:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.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 08:02:12: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:02:12: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:02:13: 5000000 INFO @ Fri, 26 Jun 2020 08:02:15: 10000000 INFO @ Fri, 26 Jun 2020 08:02:18: 1000000 INFO @ Fri, 26 Jun 2020 08:02:20: 6000000 INFO @ Fri, 26 Jun 2020 08:02:22: 11000000 INFO @ Fri, 26 Jun 2020 08:02:25: 2000000 INFO @ Fri, 26 Jun 2020 08:02:26: 7000000 INFO @ Fri, 26 Jun 2020 08:02:28: 12000000 INFO @ Fri, 26 Jun 2020 08:02:31: 3000000 INFO @ Fri, 26 Jun 2020 08:02:32: 8000000 INFO @ Fri, 26 Jun 2020 08:02:35: 13000000 INFO @ Fri, 26 Jun 2020 08:02:37: 4000000 INFO @ Fri, 26 Jun 2020 08:02:38: 9000000 INFO @ Fri, 26 Jun 2020 08:02:41: 14000000 INFO @ Fri, 26 Jun 2020 08:02:44: 5000000 INFO @ Fri, 26 Jun 2020 08:02:44: 10000000 INFO @ Fri, 26 Jun 2020 08:02:48: 15000000 INFO @ Fri, 26 Jun 2020 08:02:50: 6000000 INFO @ Fri, 26 Jun 2020 08:02:51: 11000000 INFO @ Fri, 26 Jun 2020 08:02:54: 16000000 INFO @ Fri, 26 Jun 2020 08:02:57: 7000000 INFO @ Fri, 26 Jun 2020 08:02:57: 12000000 INFO @ Fri, 26 Jun 2020 08:03:01: 17000000 INFO @ Fri, 26 Jun 2020 08:03:03: 8000000 INFO @ Fri, 26 Jun 2020 08:03:03: 13000000 INFO @ Fri, 26 Jun 2020 08:03:08: 18000000 INFO @ Fri, 26 Jun 2020 08:03:10: 14000000 INFO @ Fri, 26 Jun 2020 08:03:10: 9000000 INFO @ Fri, 26 Jun 2020 08:03:15: 19000000 INFO @ Fri, 26 Jun 2020 08:03:16: 15000000 INFO @ Fri, 26 Jun 2020 08:03:17: 10000000 INFO @ Fri, 26 Jun 2020 08:03:22: 20000000 INFO @ Fri, 26 Jun 2020 08:03:22: 16000000 INFO @ Fri, 26 Jun 2020 08:03:24: 11000000 INFO @ Fri, 26 Jun 2020 08:03:28: 17000000 INFO @ Fri, 26 Jun 2020 08:03:29: 21000000 INFO @ Fri, 26 Jun 2020 08:03:31: 12000000 INFO @ Fri, 26 Jun 2020 08:03:34: 18000000 INFO @ Fri, 26 Jun 2020 08:03:36: 22000000 INFO @ Fri, 26 Jun 2020 08:03:37: 13000000 INFO @ Fri, 26 Jun 2020 08:03:41: 19000000 INFO @ Fri, 26 Jun 2020 08:03:42: 23000000 INFO @ Fri, 26 Jun 2020 08:03:44: 14000000 INFO @ Fri, 26 Jun 2020 08:03:46: 20000000 INFO @ Fri, 26 Jun 2020 08:03:49: 24000000 INFO @ Fri, 26 Jun 2020 08:03:50: 15000000 INFO @ Fri, 26 Jun 2020 08:03:53: 21000000 INFO @ Fri, 26 Jun 2020 08:03:56: 25000000 INFO @ Fri, 26 Jun 2020 08:03:57: 16000000 INFO @ Fri, 26 Jun 2020 08:03:59: 22000000 INFO @ Fri, 26 Jun 2020 08:04:02: 26000000 INFO @ Fri, 26 Jun 2020 08:04:04: 17000000 INFO @ Fri, 26 Jun 2020 08:04:05: 23000000 INFO @ Fri, 26 Jun 2020 08:04:09: 27000000 INFO @ Fri, 26 Jun 2020 08:04:11: 18000000 INFO @ Fri, 26 Jun 2020 08:04:12: 24000000 INFO @ Fri, 26 Jun 2020 08:04:15: 28000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:04:18: 25000000 INFO @ Fri, 26 Jun 2020 08:04:18: 19000000 INFO @ Fri, 26 Jun 2020 08:04:22: 29000000 INFO @ Fri, 26 Jun 2020 08:04:23: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 08:04:23: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 08:04:23: #1 total tags in treatment: 13155313 INFO @ Fri, 26 Jun 2020 08:04:23: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:04:23: #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 08:04:23: #1 tags after filtering in treatment: 11614894 INFO @ Fri, 26 Jun 2020 08:04:23: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 08:04:23: #1 finished! INFO @ Fri, 26 Jun 2020 08:04:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:04:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:04:24: #2 number of paired peaks: 257 WARNING @ Fri, 26 Jun 2020 08:04:24: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Fri, 26 Jun 2020 08:04:24: start model_add_line... INFO @ Fri, 26 Jun 2020 08:04:24: start X-correlation... INFO @ Fri, 26 Jun 2020 08:04:24: end of X-cor INFO @ Fri, 26 Jun 2020 08:04:24: #2 finished! INFO @ Fri, 26 Jun 2020 08:04:24: #2 predicted fragment length is 105 bps INFO @ Fri, 26 Jun 2020 08:04:24: #2 alternative fragment length(s) may be 3,105,116,188 bps INFO @ Fri, 26 Jun 2020 08:04:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.05_model.r INFO @ Fri, 26 Jun 2020 08:04:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:04:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:04:24: 26000000 INFO @ Fri, 26 Jun 2020 08:04:25: 20000000 INFO @ Fri, 26 Jun 2020 08:04:30: 27000000 INFO @ Fri, 26 Jun 2020 08:04:33: 21000000 INFO @ Fri, 26 Jun 2020 08:04:36: 28000000 INFO @ Fri, 26 Jun 2020 08:04:39: 22000000 INFO @ Fri, 26 Jun 2020 08:04:42: 29000000 INFO @ Fri, 26 Jun 2020 08:04:42: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 08:04:42: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 08:04:42: #1 total tags in treatment: 13155313 INFO @ Fri, 26 Jun 2020 08:04:42: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:04:42: #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 08:04:43: #1 tags after filtering in treatment: 11614894 INFO @ Fri, 26 Jun 2020 08:04:43: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 08:04:43: #1 finished! INFO @ Fri, 26 Jun 2020 08:04:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:04:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:04:43: #2 number of paired peaks: 257 WARNING @ Fri, 26 Jun 2020 08:04:44: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Fri, 26 Jun 2020 08:04:44: start model_add_line... INFO @ Fri, 26 Jun 2020 08:04:44: start X-correlation... INFO @ Fri, 26 Jun 2020 08:04:44: end of X-cor INFO @ Fri, 26 Jun 2020 08:04:44: #2 finished! INFO @ Fri, 26 Jun 2020 08:04:44: #2 predicted fragment length is 105 bps INFO @ Fri, 26 Jun 2020 08:04:44: #2 alternative fragment length(s) may be 3,105,116,188 bps INFO @ Fri, 26 Jun 2020 08:04:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.10_model.r INFO @ Fri, 26 Jun 2020 08:04:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:04:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:04:46: 23000000 INFO @ Fri, 26 Jun 2020 08:04:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:04:52: 24000000 INFO @ Fri, 26 Jun 2020 08:04:58: 25000000 INFO @ Fri, 26 Jun 2020 08:05:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:05:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:05:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.05_summits.bed INFO @ Fri, 26 Jun 2020 08:05:01: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (433 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:05:04: 26000000 INFO @ Fri, 26 Jun 2020 08:05:07: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:05:10: 27000000 INFO @ Fri, 26 Jun 2020 08:05:16: 28000000 INFO @ Fri, 26 Jun 2020 08:05:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:05:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:05:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.10_summits.bed INFO @ Fri, 26 Jun 2020 08:05:19: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (273 records, 4 fields): 34 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:05:22: 29000000 INFO @ Fri, 26 Jun 2020 08:05:22: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 08:05:22: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 08:05:22: #1 total tags in treatment: 13155313 INFO @ Fri, 26 Jun 2020 08:05:22: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:05:22: #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 08:05:23: #1 tags after filtering in treatment: 11614894 INFO @ Fri, 26 Jun 2020 08:05:23: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 08:05:23: #1 finished! INFO @ Fri, 26 Jun 2020 08:05:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:05:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:05:24: #2 number of paired peaks: 257 WARNING @ Fri, 26 Jun 2020 08:05:24: Fewer paired peaks (257) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 257 pairs to build model! INFO @ Fri, 26 Jun 2020 08:05:24: start model_add_line... INFO @ Fri, 26 Jun 2020 08:05:24: start X-correlation... INFO @ Fri, 26 Jun 2020 08:05:24: end of X-cor INFO @ Fri, 26 Jun 2020 08:05:24: #2 finished! INFO @ Fri, 26 Jun 2020 08:05:24: #2 predicted fragment length is 105 bps INFO @ Fri, 26 Jun 2020 08:05:24: #2 alternative fragment length(s) may be 3,105,116,188 bps INFO @ Fri, 26 Jun 2020 08:05:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.20_model.r INFO @ Fri, 26 Jun 2020 08:05:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:05:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:05:47: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:05:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:05:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:05:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085354/SRX4085354.20_summits.bed INFO @ Fri, 26 Jun 2020 08:05:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (149 records, 4 fields): 1 millis CompletedMACS2peakCalling