Job ID = 6507798 SRX = SRX4085437 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T14:03:57 prefetch.2.10.7: 1) Downloading 'SRR7167466'... 2020-06-26T14:03:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:08:51 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:08:51 prefetch.2.10.7: 1) 'SRR7167466' was downloaded successfully Read 27216896 spots for SRR7167466/SRR7167466.sra Written 27216896 spots for SRR7167466/SRR7167466.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: 00:14:43 27216896 reads; of these: 27216896 (100.00%) were paired; of these: 15864029 (58.29%) aligned concordantly 0 times 9452789 (34.73%) aligned concordantly exactly 1 time 1900078 (6.98%) aligned concordantly >1 times ---- 15864029 pairs aligned concordantly 0 times; of these: 140394 (0.88%) aligned discordantly 1 time ---- 15723635 pairs aligned 0 times concordantly or discordantly; of these: 31447270 mates make up the pairs; of these: 28202504 (89.68%) aligned 0 times 2842410 (9.04%) aligned exactly 1 time 402356 (1.28%) aligned >1 times 48.19% overall alignment rate Time searching: 00:14:43 Overall time: 00:14:43 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] 1581900 / 11451915 = 0.1381 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 23:34:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.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 23:34:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:34:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:34:22: 1000000 INFO @ Fri, 26 Jun 2020 23:34:29: 2000000 INFO @ Fri, 26 Jun 2020 23:34:36: 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 23:34:43: 4000000 INFO @ Fri, 26 Jun 2020 23:34:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.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 23:34:45: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:34:45: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:34:50: 5000000 INFO @ Fri, 26 Jun 2020 23:34:52: 1000000 INFO @ Fri, 26 Jun 2020 23:34:58: 6000000 INFO @ Fri, 26 Jun 2020 23:35:00: 2000000 INFO @ Fri, 26 Jun 2020 23:35:06: 7000000 INFO @ Fri, 26 Jun 2020 23:35:07: 3000000 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 23:35:13: 8000000 INFO @ Fri, 26 Jun 2020 23:35:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.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 23:35:15: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:35:15: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:35:15: 4000000 INFO @ Fri, 26 Jun 2020 23:35:21: 9000000 INFO @ Fri, 26 Jun 2020 23:35:23: 1000000 INFO @ Fri, 26 Jun 2020 23:35:23: 5000000 INFO @ Fri, 26 Jun 2020 23:35:29: 10000000 INFO @ Fri, 26 Jun 2020 23:35:31: 2000000 INFO @ Fri, 26 Jun 2020 23:35:31: 6000000 INFO @ Fri, 26 Jun 2020 23:35:37: 11000000 INFO @ Fri, 26 Jun 2020 23:35:39: 7000000 INFO @ Fri, 26 Jun 2020 23:35:39: 3000000 INFO @ Fri, 26 Jun 2020 23:35:44: 12000000 INFO @ Fri, 26 Jun 2020 23:35:47: 8000000 INFO @ Fri, 26 Jun 2020 23:35:47: 4000000 INFO @ Fri, 26 Jun 2020 23:35:52: 13000000 INFO @ Fri, 26 Jun 2020 23:35:55: 9000000 INFO @ Fri, 26 Jun 2020 23:35:55: 5000000 INFO @ Fri, 26 Jun 2020 23:35:59: 14000000 INFO @ Fri, 26 Jun 2020 23:36:03: 10000000 INFO @ Fri, 26 Jun 2020 23:36:03: 6000000 INFO @ Fri, 26 Jun 2020 23:36:07: 15000000 INFO @ Fri, 26 Jun 2020 23:36:11: 7000000 INFO @ Fri, 26 Jun 2020 23:36:11: 11000000 INFO @ Fri, 26 Jun 2020 23:36:14: 16000000 INFO @ Fri, 26 Jun 2020 23:36:19: 8000000 INFO @ Fri, 26 Jun 2020 23:36:19: 12000000 INFO @ Fri, 26 Jun 2020 23:36:22: 17000000 INFO @ Fri, 26 Jun 2020 23:36:27: 9000000 INFO @ Fri, 26 Jun 2020 23:36:27: 13000000 INFO @ Fri, 26 Jun 2020 23:36:30: 18000000 INFO @ Fri, 26 Jun 2020 23:36:35: 10000000 INFO @ Fri, 26 Jun 2020 23:36:35: 14000000 INFO @ Fri, 26 Jun 2020 23:36:37: 19000000 INFO @ Fri, 26 Jun 2020 23:36:43: 11000000 INFO @ Fri, 26 Jun 2020 23:36:43: 15000000 INFO @ Fri, 26 Jun 2020 23:36:45: 20000000 INFO @ Fri, 26 Jun 2020 23:36:51: 12000000 INFO @ Fri, 26 Jun 2020 23:36:51: 16000000 INFO @ Fri, 26 Jun 2020 23:36:52: 21000000 INFO @ Fri, 26 Jun 2020 23:36:59: 13000000 INFO @ Fri, 26 Jun 2020 23:36:59: 17000000 INFO @ Fri, 26 Jun 2020 23:37:00: 22000000 INFO @ Fri, 26 Jun 2020 23:37:07: 14000000 INFO @ Fri, 26 Jun 2020 23:37:07: 18000000 INFO @ Fri, 26 Jun 2020 23:37:07: 23000000 INFO @ Fri, 26 Jun 2020 23:37:08: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 23:37:08: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 23:37:08: #1 total tags in treatment: 9780450 INFO @ Fri, 26 Jun 2020 23:37:08: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:37:08: #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 23:37:08: #1 tags after filtering in treatment: 8672777 INFO @ Fri, 26 Jun 2020 23:37:08: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 26 Jun 2020 23:37:08: #1 finished! INFO @ Fri, 26 Jun 2020 23:37:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:37:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:37:08: #2 number of paired peaks: 335 WARNING @ Fri, 26 Jun 2020 23:37:08: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Fri, 26 Jun 2020 23:37:08: start model_add_line... INFO @ Fri, 26 Jun 2020 23:37:09: start X-correlation... INFO @ Fri, 26 Jun 2020 23:37:09: end of X-cor INFO @ Fri, 26 Jun 2020 23:37:09: #2 finished! INFO @ Fri, 26 Jun 2020 23:37:09: #2 predicted fragment length is 128 bps INFO @ Fri, 26 Jun 2020 23:37:09: #2 alternative fragment length(s) may be 128,598 bps INFO @ Fri, 26 Jun 2020 23:37:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.05_model.r INFO @ Fri, 26 Jun 2020 23:37:09: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:37:09: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:37:14: 15000000 INFO @ Fri, 26 Jun 2020 23:37:14: 19000000 INFO @ Fri, 26 Jun 2020 23:37:21: 16000000 INFO @ Fri, 26 Jun 2020 23:37:21: 20000000 INFO @ Fri, 26 Jun 2020 23:37:28: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:37:28: 17000000 INFO @ Fri, 26 Jun 2020 23:37:29: 21000000 INFO @ Fri, 26 Jun 2020 23:37:36: 18000000 INFO @ Fri, 26 Jun 2020 23:37:36: 22000000 INFO @ Fri, 26 Jun 2020 23:37:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:37:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:37:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.05_summits.bed INFO @ Fri, 26 Jun 2020 23:37:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2039 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:37:43: 23000000 INFO @ Fri, 26 Jun 2020 23:37:43: 19000000 INFO @ Fri, 26 Jun 2020 23:37:44: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 23:37:44: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 23:37:44: #1 total tags in treatment: 9780450 INFO @ Fri, 26 Jun 2020 23:37:44: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:37:44: #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 23:37:44: #1 tags after filtering in treatment: 8672777 INFO @ Fri, 26 Jun 2020 23:37:44: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 26 Jun 2020 23:37:44: #1 finished! INFO @ Fri, 26 Jun 2020 23:37:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:37:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:37:44: #2 number of paired peaks: 335 WARNING @ Fri, 26 Jun 2020 23:37:44: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Fri, 26 Jun 2020 23:37:44: start model_add_line... INFO @ Fri, 26 Jun 2020 23:37:44: start X-correlation... INFO @ Fri, 26 Jun 2020 23:37:44: end of X-cor INFO @ Fri, 26 Jun 2020 23:37:44: #2 finished! INFO @ Fri, 26 Jun 2020 23:37:44: #2 predicted fragment length is 128 bps INFO @ Fri, 26 Jun 2020 23:37:44: #2 alternative fragment length(s) may be 128,598 bps INFO @ Fri, 26 Jun 2020 23:37:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.10_model.r INFO @ Fri, 26 Jun 2020 23:37:45: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:37:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:37:50: 20000000 INFO @ Fri, 26 Jun 2020 23:37:57: 21000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:38:04: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:38:04: 22000000 INFO @ Fri, 26 Jun 2020 23:38:11: 23000000 INFO @ Fri, 26 Jun 2020 23:38:11: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 23:38:11: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 23:38:11: #1 total tags in treatment: 9780450 INFO @ Fri, 26 Jun 2020 23:38:11: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:38:11: #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 23:38:11: #1 tags after filtering in treatment: 8672777 INFO @ Fri, 26 Jun 2020 23:38:11: #1 Redundant rate of treatment: 0.11 INFO @ Fri, 26 Jun 2020 23:38:11: #1 finished! INFO @ Fri, 26 Jun 2020 23:38:11: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:38:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:38:12: #2 number of paired peaks: 335 WARNING @ Fri, 26 Jun 2020 23:38:12: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Fri, 26 Jun 2020 23:38:12: start model_add_line... INFO @ Fri, 26 Jun 2020 23:38:12: start X-correlation... INFO @ Fri, 26 Jun 2020 23:38:12: end of X-cor INFO @ Fri, 26 Jun 2020 23:38:12: #2 finished! INFO @ Fri, 26 Jun 2020 23:38:12: #2 predicted fragment length is 128 bps INFO @ Fri, 26 Jun 2020 23:38:12: #2 alternative fragment length(s) may be 128,598 bps INFO @ Fri, 26 Jun 2020 23:38:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.20_model.r INFO @ Fri, 26 Jun 2020 23:38:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:38:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:38:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:38:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:38:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.10_summits.bed INFO @ Fri, 26 Jun 2020 23:38:14: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1139 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:38:31: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:38:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:38:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:38:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085437/SRX4085437.20_summits.bed INFO @ Fri, 26 Jun 2020 23:38:40: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (484 records, 4 fields): 2 millis CompletedMACS2peakCalling