Job ID = 6507729 SRX = SRX1353666 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T13:32:33 prefetch.2.10.7: 1) Downloading 'SRR2722820'... 2020-06-26T13:32:33 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T13:34:25 prefetch.2.10.7: HTTPS download succeed 2020-06-26T13:34:25 prefetch.2.10.7: 1) 'SRR2722820' was downloaded successfully Read 14547030 spots for SRR2722820/SRR2722820.sra Written 14547030 spots for SRR2722820/SRR2722820.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: 00:14:53 14547030 reads; of these: 14547030 (100.00%) were paired; of these: 668124 (4.59%) aligned concordantly 0 times 11611654 (79.82%) aligned concordantly exactly 1 time 2267252 (15.59%) aligned concordantly >1 times ---- 668124 pairs aligned concordantly 0 times; of these: 266260 (39.85%) aligned discordantly 1 time ---- 401864 pairs aligned 0 times concordantly or discordantly; of these: 803728 mates make up the pairs; of these: 477495 (59.41%) aligned 0 times 192248 (23.92%) aligned exactly 1 time 133985 (16.67%) aligned >1 times 98.36% overall alignment rate Time searching: 00:14:53 Overall time: 00:14:53 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 12 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] 271169 / 14073103 = 0.0193 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 23:00:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.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 23:00:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:00:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:01:04: 1000000 INFO @ Fri, 26 Jun 2020 23:01:10: 2000000 INFO @ Fri, 26 Jun 2020 23:01:16: 3000000 INFO @ Fri, 26 Jun 2020 23:01:21: 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 23:01:27: 5000000 INFO @ Fri, 26 Jun 2020 23:01:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.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 23:01:31: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:01:31: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:01:33: 6000000 INFO @ Fri, 26 Jun 2020 23:01:37: 1000000 INFO @ Fri, 26 Jun 2020 23:01:39: 7000000 INFO @ Fri, 26 Jun 2020 23:01:44: 2000000 INFO @ Fri, 26 Jun 2020 23:01:45: 8000000 INFO @ Fri, 26 Jun 2020 23:01:50: 3000000 INFO @ Fri, 26 Jun 2020 23:01:51: 9000000 INFO @ Fri, 26 Jun 2020 23:01:56: 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 23:01:57: 10000000 INFO @ Fri, 26 Jun 2020 23:01:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.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 23:01:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:01:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:02:02: 5000000 INFO @ Fri, 26 Jun 2020 23:02:04: 11000000 INFO @ Fri, 26 Jun 2020 23:02:04: 1000000 INFO @ Fri, 26 Jun 2020 23:02:08: 6000000 INFO @ Fri, 26 Jun 2020 23:02:10: 12000000 INFO @ Fri, 26 Jun 2020 23:02:10: 2000000 INFO @ Fri, 26 Jun 2020 23:02:14: 7000000 INFO @ Fri, 26 Jun 2020 23:02:16: 13000000 INFO @ Fri, 26 Jun 2020 23:02:16: 3000000 INFO @ Fri, 26 Jun 2020 23:02:20: 8000000 INFO @ Fri, 26 Jun 2020 23:02:22: 14000000 INFO @ Fri, 26 Jun 2020 23:02:22: 4000000 INFO @ Fri, 26 Jun 2020 23:02:26: 9000000 INFO @ Fri, 26 Jun 2020 23:02:28: 5000000 INFO @ Fri, 26 Jun 2020 23:02:28: 15000000 INFO @ Fri, 26 Jun 2020 23:02:32: 10000000 INFO @ Fri, 26 Jun 2020 23:02:34: 6000000 INFO @ Fri, 26 Jun 2020 23:02:34: 16000000 INFO @ Fri, 26 Jun 2020 23:02:38: 11000000 INFO @ Fri, 26 Jun 2020 23:02:40: 7000000 INFO @ Fri, 26 Jun 2020 23:02:40: 17000000 INFO @ Fri, 26 Jun 2020 23:02:45: 12000000 INFO @ Fri, 26 Jun 2020 23:02:46: 8000000 INFO @ Fri, 26 Jun 2020 23:02:46: 18000000 INFO @ Fri, 26 Jun 2020 23:02:51: 13000000 INFO @ Fri, 26 Jun 2020 23:02:52: 9000000 INFO @ Fri, 26 Jun 2020 23:02:53: 19000000 INFO @ Fri, 26 Jun 2020 23:02:57: 14000000 INFO @ Fri, 26 Jun 2020 23:02:58: 10000000 INFO @ Fri, 26 Jun 2020 23:02:59: 20000000 INFO @ Fri, 26 Jun 2020 23:03:04: 15000000 INFO @ Fri, 26 Jun 2020 23:03:04: 11000000 INFO @ Fri, 26 Jun 2020 23:03:06: 21000000 INFO @ Fri, 26 Jun 2020 23:03:10: 16000000 INFO @ Fri, 26 Jun 2020 23:03:10: 12000000 INFO @ Fri, 26 Jun 2020 23:03:12: 22000000 INFO @ Fri, 26 Jun 2020 23:03:16: 13000000 INFO @ Fri, 26 Jun 2020 23:03:16: 17000000 INFO @ Fri, 26 Jun 2020 23:03:18: 23000000 INFO @ Fri, 26 Jun 2020 23:03:22: 14000000 INFO @ Fri, 26 Jun 2020 23:03:23: 18000000 INFO @ Fri, 26 Jun 2020 23:03:25: 24000000 INFO @ Fri, 26 Jun 2020 23:03:28: 15000000 INFO @ Fri, 26 Jun 2020 23:03:29: 19000000 INFO @ Fri, 26 Jun 2020 23:03:31: 25000000 INFO @ Fri, 26 Jun 2020 23:03:34: 16000000 INFO @ Fri, 26 Jun 2020 23:03:36: 20000000 INFO @ Fri, 26 Jun 2020 23:03:37: 26000000 INFO @ Fri, 26 Jun 2020 23:03:39: 17000000 INFO @ Fri, 26 Jun 2020 23:03:42: 21000000 INFO @ Fri, 26 Jun 2020 23:03:44: 27000000 INFO @ Fri, 26 Jun 2020 23:03:45: 18000000 INFO @ Fri, 26 Jun 2020 23:03:49: 22000000 INFO @ Fri, 26 Jun 2020 23:03:50: 28000000 INFO @ Fri, 26 Jun 2020 23:03:51: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:03:51: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:03:51: #1 total tags in treatment: 13608959 INFO @ Fri, 26 Jun 2020 23:03:51: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:03:51: #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 23:03:51: #1 tags after filtering in treatment: 12538764 INFO @ Fri, 26 Jun 2020 23:03:51: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 23:03:51: #1 finished! INFO @ Fri, 26 Jun 2020 23:03:51: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:03:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:03:51: 19000000 INFO @ Fri, 26 Jun 2020 23:03:52: #2 number of paired peaks: 349 WARNING @ Fri, 26 Jun 2020 23:03:52: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Fri, 26 Jun 2020 23:03:52: start model_add_line... INFO @ Fri, 26 Jun 2020 23:03:52: start X-correlation... INFO @ Fri, 26 Jun 2020 23:03:52: end of X-cor INFO @ Fri, 26 Jun 2020 23:03:52: #2 finished! INFO @ Fri, 26 Jun 2020 23:03:52: #2 predicted fragment length is 134 bps INFO @ Fri, 26 Jun 2020 23:03:52: #2 alternative fragment length(s) may be 4,134,164 bps INFO @ Fri, 26 Jun 2020 23:03:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.05_model.r INFO @ Fri, 26 Jun 2020 23:03:52: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:03:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:03:55: 23000000 INFO @ Fri, 26 Jun 2020 23:03:57: 20000000 INFO @ Fri, 26 Jun 2020 23:04:02: 24000000 INFO @ Fri, 26 Jun 2020 23:04:03: 21000000 INFO @ Fri, 26 Jun 2020 23:04:08: 25000000 INFO @ Fri, 26 Jun 2020 23:04:08: 22000000 INFO @ Fri, 26 Jun 2020 23:04:14: 23000000 INFO @ Fri, 26 Jun 2020 23:04:14: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:04:19: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:04:20: 24000000 INFO @ Fri, 26 Jun 2020 23:04:21: 27000000 INFO @ Fri, 26 Jun 2020 23:04:26: 25000000 INFO @ Fri, 26 Jun 2020 23:04:27: 28000000 INFO @ Fri, 26 Jun 2020 23:04:28: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:04:28: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:04:28: #1 total tags in treatment: 13608959 INFO @ Fri, 26 Jun 2020 23:04:28: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:04:28: #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 23:04:28: #1 tags after filtering in treatment: 12538764 INFO @ Fri, 26 Jun 2020 23:04:28: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 23:04:28: #1 finished! INFO @ Fri, 26 Jun 2020 23:04:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:04:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:04:29: #2 number of paired peaks: 349 WARNING @ Fri, 26 Jun 2020 23:04:29: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Fri, 26 Jun 2020 23:04:29: start model_add_line... INFO @ Fri, 26 Jun 2020 23:04:29: start X-correlation... INFO @ Fri, 26 Jun 2020 23:04:29: end of X-cor INFO @ Fri, 26 Jun 2020 23:04:29: #2 finished! INFO @ Fri, 26 Jun 2020 23:04:29: #2 predicted fragment length is 134 bps INFO @ Fri, 26 Jun 2020 23:04:29: #2 alternative fragment length(s) may be 4,134,164 bps INFO @ Fri, 26 Jun 2020 23:04:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.10_model.r INFO @ Fri, 26 Jun 2020 23:04:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:04:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:04:31: 26000000 INFO @ Fri, 26 Jun 2020 23:04:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:04:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:04:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.05_summits.bed INFO @ Fri, 26 Jun 2020 23:04:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (654 records, 4 fields): 57 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:04:37: 27000000 INFO @ Fri, 26 Jun 2020 23:04:42: 28000000 INFO @ Fri, 26 Jun 2020 23:04:42: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 23:04:42: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 23:04:42: #1 total tags in treatment: 13608959 INFO @ Fri, 26 Jun 2020 23:04:42: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:04:42: #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 23:04:43: #1 tags after filtering in treatment: 12538764 INFO @ Fri, 26 Jun 2020 23:04:43: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 23:04:43: #1 finished! INFO @ Fri, 26 Jun 2020 23:04:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:04:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:04:44: #2 number of paired peaks: 349 WARNING @ Fri, 26 Jun 2020 23:04:44: Fewer paired peaks (349) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 349 pairs to build model! INFO @ Fri, 26 Jun 2020 23:04:44: start model_add_line... INFO @ Fri, 26 Jun 2020 23:04:44: start X-correlation... INFO @ Fri, 26 Jun 2020 23:04:44: end of X-cor INFO @ Fri, 26 Jun 2020 23:04:44: #2 finished! INFO @ Fri, 26 Jun 2020 23:04:44: #2 predicted fragment length is 134 bps INFO @ Fri, 26 Jun 2020 23:04:44: #2 alternative fragment length(s) may be 4,134,164 bps INFO @ Fri, 26 Jun 2020 23:04:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.20_model.r INFO @ Fri, 26 Jun 2020 23:04:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:04:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:04:57: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:05:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:05:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:05:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.10_summits.bed INFO @ Fri, 26 Jun 2020 23:05:10: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (320 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:05:13: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:05:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:05:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:05:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX1353666/SRX1353666.20_summits.bed INFO @ Fri, 26 Jun 2020 23:05:26: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (203 records, 4 fields): 1 millis CompletedMACS2peakCalling