Job ID = 6497341 SRX = SRX1353666 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T21:33:36 prefetch.2.10.7: 1) Downloading 'SRR2722820'... 2020-06-25T21:33:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:35:52 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:35:52 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: 00:17:28 14547030 reads; of these: 14547030 (100.00%) were paired; of these: 668287 (4.59%) aligned concordantly 0 times 11611653 (79.82%) aligned concordantly exactly 1 time 2267090 (15.58%) aligned concordantly >1 times ---- 668287 pairs aligned concordantly 0 times; of these: 266253 (39.84%) aligned discordantly 1 time ---- 402034 pairs aligned 0 times concordantly or discordantly; of these: 804068 mates make up the pairs; of these: 477791 (59.42%) aligned 0 times 192266 (23.91%) aligned exactly 1 time 134011 (16.67%) aligned >1 times 98.36% overall alignment rate Time searching: 00:17:28 Overall time: 00:17:28 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] 271175 / 14072928 = 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 07:09:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353666/SRX1353666.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353666/SRX1353666.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353666/SRX1353666.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:09:01: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:09:01: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:09:08: 1000000 INFO @ Fri, 26 Jun 2020 07:09:14: 2000000 INFO @ Fri, 26 Jun 2020 07:09:20: 3000000 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 07:09:26: 4000000 INFO @ Fri, 26 Jun 2020 07:09:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353666/SRX1353666.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353666/SRX1353666.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353666/SRX1353666.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:09:26: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:09:26: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:09:32: 1000000 INFO @ Fri, 26 Jun 2020 07:09:33: 5000000 INFO @ Fri, 26 Jun 2020 07:09:37: 2000000 INFO @ Fri, 26 Jun 2020 07:09:39: 6000000 INFO @ Fri, 26 Jun 2020 07:09:43: 3000000 INFO @ Fri, 26 Jun 2020 07:09:45: 7000000 INFO @ Fri, 26 Jun 2020 07:09:48: 4000000 INFO @ Fri, 26 Jun 2020 07:09:52: 8000000 INFO @ Fri, 26 Jun 2020 07:09:54: 5000000 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 07:09:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1353666/SRX1353666.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1353666/SRX1353666.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1353666/SRX1353666.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/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 07:09:58: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:09:58: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:09:58: 9000000 INFO @ Fri, 26 Jun 2020 07:09:59: 6000000 INFO @ Fri, 26 Jun 2020 07:10:04: 1000000 INFO @ Fri, 26 Jun 2020 07:10:04: 10000000 INFO @ Fri, 26 Jun 2020 07:10:05: 7000000 INFO @ Fri, 26 Jun 2020 07:10:09: 2000000 INFO @ Fri, 26 Jun 2020 07:10:10: 8000000 INFO @ Fri, 26 Jun 2020 07:10:11: 11000000 INFO @ Fri, 26 Jun 2020 07:10:15: 3000000 INFO @ Fri, 26 Jun 2020 07:10:16: 9000000 INFO @ Fri, 26 Jun 2020 07:10:17: 12000000 INFO @ Fri, 26 Jun 2020 07:10:21: 4000000 INFO @ Fri, 26 Jun 2020 07:10:21: 10000000 INFO @ Fri, 26 Jun 2020 07:10:23: 13000000 INFO @ Fri, 26 Jun 2020 07:10:26: 5000000 INFO @ Fri, 26 Jun 2020 07:10:26: 11000000 INFO @ Fri, 26 Jun 2020 07:10:29: 14000000 INFO @ Fri, 26 Jun 2020 07:10:32: 12000000 INFO @ Fri, 26 Jun 2020 07:10:32: 6000000 INFO @ Fri, 26 Jun 2020 07:10:36: 15000000 INFO @ Fri, 26 Jun 2020 07:10:37: 13000000 INFO @ Fri, 26 Jun 2020 07:10:37: 7000000 INFO @ Fri, 26 Jun 2020 07:10:42: 16000000 INFO @ Fri, 26 Jun 2020 07:10:43: 14000000 INFO @ Fri, 26 Jun 2020 07:10:43: 8000000 INFO @ Fri, 26 Jun 2020 07:10:48: 17000000 INFO @ Fri, 26 Jun 2020 07:10:48: 15000000 INFO @ Fri, 26 Jun 2020 07:10:49: 9000000 INFO @ Fri, 26 Jun 2020 07:10:53: 16000000 INFO @ Fri, 26 Jun 2020 07:10:54: 10000000 INFO @ Fri, 26 Jun 2020 07:10:54: 18000000 INFO @ Fri, 26 Jun 2020 07:10:59: 17000000 INFO @ Fri, 26 Jun 2020 07:11:00: 11000000 INFO @ Fri, 26 Jun 2020 07:11:00: 19000000 INFO @ Fri, 26 Jun 2020 07:11:04: 18000000 INFO @ Fri, 26 Jun 2020 07:11:05: 12000000 INFO @ Fri, 26 Jun 2020 07:11:07: 20000000 INFO @ Fri, 26 Jun 2020 07:11:10: 19000000 INFO @ Fri, 26 Jun 2020 07:11:11: 13000000 INFO @ Fri, 26 Jun 2020 07:11:13: 21000000 INFO @ Fri, 26 Jun 2020 07:11:15: 20000000 INFO @ Fri, 26 Jun 2020 07:11:16: 14000000 INFO @ Fri, 26 Jun 2020 07:11:19: 22000000 INFO @ Fri, 26 Jun 2020 07:11:20: 21000000 INFO @ Fri, 26 Jun 2020 07:11:22: 15000000 INFO @ Fri, 26 Jun 2020 07:11:25: 23000000 INFO @ Fri, 26 Jun 2020 07:11:26: 22000000 INFO @ Fri, 26 Jun 2020 07:11:27: 16000000 INFO @ Fri, 26 Jun 2020 07:11:31: 23000000 INFO @ Fri, 26 Jun 2020 07:11:31: 24000000 INFO @ Fri, 26 Jun 2020 07:11:33: 17000000 INFO @ Fri, 26 Jun 2020 07:11:37: 24000000 INFO @ Fri, 26 Jun 2020 07:11:37: 25000000 INFO @ Fri, 26 Jun 2020 07:11:38: 18000000 INFO @ Fri, 26 Jun 2020 07:11:42: 25000000 INFO @ Fri, 26 Jun 2020 07:11:44: 26000000 INFO @ Fri, 26 Jun 2020 07:11:44: 19000000 INFO @ Fri, 26 Jun 2020 07:11:48: 26000000 INFO @ Fri, 26 Jun 2020 07:11:50: 20000000 INFO @ Fri, 26 Jun 2020 07:11:50: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:11:53: 27000000 INFO @ Fri, 26 Jun 2020 07:11:55: 21000000 INFO @ Fri, 26 Jun 2020 07:11:56: 28000000 INFO @ Fri, 26 Jun 2020 07:11:57: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:11:57: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:11:57: #1 total tags in treatment: 13608791 INFO @ Fri, 26 Jun 2020 07:11:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:11:57: #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 07:11:57: #1 tags after filtering in treatment: 12538669 INFO @ Fri, 26 Jun 2020 07:11:57: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 07:11:57: #1 finished! INFO @ Fri, 26 Jun 2020 07:11:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:11:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:11:58: #2 number of paired peaks: 348 WARNING @ Fri, 26 Jun 2020 07:11:58: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Fri, 26 Jun 2020 07:11:58: start model_add_line... INFO @ Fri, 26 Jun 2020 07:11:58: start X-correlation... INFO @ Fri, 26 Jun 2020 07:11:58: end of X-cor INFO @ Fri, 26 Jun 2020 07:11:58: #2 finished! INFO @ Fri, 26 Jun 2020 07:11:58: #2 predicted fragment length is 135 bps INFO @ Fri, 26 Jun 2020 07:11:58: #2 alternative fragment length(s) may be 4,135,163 bps INFO @ Fri, 26 Jun 2020 07:11:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353666/SRX1353666.05_model.r INFO @ Fri, 26 Jun 2020 07:11:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:11:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:11:58: 28000000 INFO @ Fri, 26 Jun 2020 07:11:59: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:11:59: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:11:59: #1 total tags in treatment: 13608791 INFO @ Fri, 26 Jun 2020 07:11:59: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:11:59: #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 07:11:59: #1 tags after filtering in treatment: 12538669 INFO @ Fri, 26 Jun 2020 07:11:59: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 07:11:59: #1 finished! INFO @ Fri, 26 Jun 2020 07:11:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:11:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:12:00: #2 number of paired peaks: 348 WARNING @ Fri, 26 Jun 2020 07:12:00: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Fri, 26 Jun 2020 07:12:00: start model_add_line... INFO @ Fri, 26 Jun 2020 07:12:00: start X-correlation... INFO @ Fri, 26 Jun 2020 07:12:00: end of X-cor INFO @ Fri, 26 Jun 2020 07:12:00: #2 finished! INFO @ Fri, 26 Jun 2020 07:12:00: #2 predicted fragment length is 135 bps INFO @ Fri, 26 Jun 2020 07:12:00: #2 alternative fragment length(s) may be 4,135,163 bps INFO @ Fri, 26 Jun 2020 07:12:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353666/SRX1353666.10_model.r INFO @ Fri, 26 Jun 2020 07:12:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:12:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:12:01: 22000000 INFO @ Fri, 26 Jun 2020 07:12:06: 23000000 INFO @ Fri, 26 Jun 2020 07:12:11: 24000000 INFO @ Fri, 26 Jun 2020 07:12:16: 25000000 INFO @ Fri, 26 Jun 2020 07:12:21: 26000000 INFO @ Fri, 26 Jun 2020 07:12:23: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:12:26: 27000000 INFO @ Fri, 26 Jun 2020 07:12:26: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:12:31: 28000000 INFO @ Fri, 26 Jun 2020 07:12:31: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:12:31: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:12:31: #1 total tags in treatment: 13608791 INFO @ Fri, 26 Jun 2020 07:12:31: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:12:31: #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 07:12:31: #1 tags after filtering in treatment: 12538669 INFO @ Fri, 26 Jun 2020 07:12:31: #1 Redundant rate of treatment: 0.08 INFO @ Fri, 26 Jun 2020 07:12:31: #1 finished! INFO @ Fri, 26 Jun 2020 07:12:31: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:12:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:12:32: #2 number of paired peaks: 348 WARNING @ Fri, 26 Jun 2020 07:12:32: Fewer paired peaks (348) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 348 pairs to build model! INFO @ Fri, 26 Jun 2020 07:12:32: start model_add_line... INFO @ Fri, 26 Jun 2020 07:12:32: start X-correlation... INFO @ Fri, 26 Jun 2020 07:12:32: end of X-cor INFO @ Fri, 26 Jun 2020 07:12:32: #2 finished! INFO @ Fri, 26 Jun 2020 07:12:32: #2 predicted fragment length is 135 bps INFO @ Fri, 26 Jun 2020 07:12:32: #2 alternative fragment length(s) may be 4,135,163 bps INFO @ Fri, 26 Jun 2020 07:12:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1353666/SRX1353666.20_model.r INFO @ Fri, 26 Jun 2020 07:12:32: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:12:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:12:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353666/SRX1353666.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:12:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353666/SRX1353666.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:12:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353666/SRX1353666.05_summits.bed INFO @ Fri, 26 Jun 2020 07:12:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (641 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:12:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353666/SRX1353666.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:12:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353666/SRX1353666.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:12:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353666/SRX1353666.10_summits.bed INFO @ Fri, 26 Jun 2020 07:12:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (317 records, 4 fields): 71 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:12:58: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:13:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1353666/SRX1353666.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:13:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1353666/SRX1353666.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:13:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1353666/SRX1353666.20_summits.bed INFO @ Fri, 26 Jun 2020 07:13:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (208 records, 4 fields): 1 millis CompletedMACS2peakCalling