Job ID = 6367868 SRX = SRX4085435 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:38:59 prefetch.2.10.7: 1) Downloading 'SRR7167464'... 2020-06-15T23:38:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:48:44 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:48:44 prefetch.2.10.7: 1) 'SRR7167464' was downloaded successfully Read 25917677 spots for SRR7167464/SRR7167464.sra Written 25917677 spots for SRR7167464/SRR7167464.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: 00:14:48 25917677 reads; of these: 25917677 (100.00%) were paired; of these: 12013381 (46.35%) aligned concordantly 0 times 11872879 (45.81%) aligned concordantly exactly 1 time 2031417 (7.84%) aligned concordantly >1 times ---- 12013381 pairs aligned concordantly 0 times; of these: 156540 (1.30%) aligned discordantly 1 time ---- 11856841 pairs aligned 0 times concordantly or discordantly; of these: 23713682 mates make up the pairs; of these: 20607116 (86.90%) aligned 0 times 2679831 (11.30%) aligned exactly 1 time 426735 (1.80%) aligned >1 times 60.25% overall alignment rate Time searching: 00:14:49 Overall time: 00:14:49 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 16 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] 2615490 / 14018326 = 0.1866 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 @ Tue, 16 Jun 2020 09:14:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.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 @ Tue, 16 Jun 2020 09:14:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:14:31: 1000000 INFO @ Tue, 16 Jun 2020 09:14:37: 2000000 INFO @ Tue, 16 Jun 2020 09:14:43: 3000000 INFO @ Tue, 16 Jun 2020 09:14:48: 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 @ Tue, 16 Jun 2020 09:14:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.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 @ Tue, 16 Jun 2020 09:14:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:14:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:14:54: 5000000 INFO @ Tue, 16 Jun 2020 09:15:01: 6000000 INFO @ Tue, 16 Jun 2020 09:15:02: 1000000 INFO @ Tue, 16 Jun 2020 09:15:09: 7000000 INFO @ Tue, 16 Jun 2020 09:15:09: 2000000 INFO @ Tue, 16 Jun 2020 09:15:16: 8000000 INFO @ Tue, 16 Jun 2020 09:15:17: 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 @ Tue, 16 Jun 2020 09:15:23: 9000000 INFO @ Tue, 16 Jun 2020 09:15:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.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 @ Tue, 16 Jun 2020 09:15:24: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:15:24: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:15:25: 4000000 INFO @ Tue, 16 Jun 2020 09:15:31: 10000000 INFO @ Tue, 16 Jun 2020 09:15:32: 1000000 INFO @ Tue, 16 Jun 2020 09:15:33: 5000000 INFO @ Tue, 16 Jun 2020 09:15:38: 11000000 INFO @ Tue, 16 Jun 2020 09:15:39: 2000000 INFO @ Tue, 16 Jun 2020 09:15:41: 6000000 INFO @ Tue, 16 Jun 2020 09:15:46: 12000000 INFO @ Tue, 16 Jun 2020 09:15:47: 3000000 INFO @ Tue, 16 Jun 2020 09:15:49: 7000000 INFO @ Tue, 16 Jun 2020 09:15:54: 13000000 INFO @ Tue, 16 Jun 2020 09:15:55: 4000000 INFO @ Tue, 16 Jun 2020 09:15:57: 8000000 INFO @ Tue, 16 Jun 2020 09:16:01: 14000000 INFO @ Tue, 16 Jun 2020 09:16:02: 5000000 INFO @ Tue, 16 Jun 2020 09:16:05: 9000000 INFO @ Tue, 16 Jun 2020 09:16:09: 15000000 INFO @ Tue, 16 Jun 2020 09:16:10: 6000000 INFO @ Tue, 16 Jun 2020 09:16:13: 10000000 INFO @ Tue, 16 Jun 2020 09:16:16: 16000000 INFO @ Tue, 16 Jun 2020 09:16:17: 7000000 INFO @ Tue, 16 Jun 2020 09:16:21: 11000000 INFO @ Tue, 16 Jun 2020 09:16:24: 17000000 INFO @ Tue, 16 Jun 2020 09:16:25: 8000000 INFO @ Tue, 16 Jun 2020 09:16:29: 12000000 INFO @ Tue, 16 Jun 2020 09:16:32: 18000000 INFO @ Tue, 16 Jun 2020 09:16:33: 9000000 INFO @ Tue, 16 Jun 2020 09:16:36: 13000000 INFO @ Tue, 16 Jun 2020 09:16:39: 19000000 INFO @ Tue, 16 Jun 2020 09:16:40: 10000000 INFO @ Tue, 16 Jun 2020 09:16:44: 14000000 INFO @ Tue, 16 Jun 2020 09:16:47: 20000000 INFO @ Tue, 16 Jun 2020 09:16:48: 11000000 INFO @ Tue, 16 Jun 2020 09:16:52: 15000000 INFO @ Tue, 16 Jun 2020 09:16:54: 21000000 INFO @ Tue, 16 Jun 2020 09:16:55: 12000000 INFO @ Tue, 16 Jun 2020 09:17:00: 16000000 INFO @ Tue, 16 Jun 2020 09:17:02: 22000000 INFO @ Tue, 16 Jun 2020 09:17:03: 13000000 INFO @ Tue, 16 Jun 2020 09:17:08: 17000000 INFO @ Tue, 16 Jun 2020 09:17:09: 23000000 INFO @ Tue, 16 Jun 2020 09:17:11: 14000000 INFO @ Tue, 16 Jun 2020 09:17:15: 18000000 INFO @ Tue, 16 Jun 2020 09:17:17: 24000000 INFO @ Tue, 16 Jun 2020 09:17:18: 15000000 INFO @ Tue, 16 Jun 2020 09:17:23: 19000000 INFO @ Tue, 16 Jun 2020 09:17:25: 25000000 INFO @ Tue, 16 Jun 2020 09:17:26: 16000000 INFO @ Tue, 16 Jun 2020 09:17:31: 20000000 INFO @ Tue, 16 Jun 2020 09:17:31: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:17:31: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:17:31: #1 total tags in treatment: 11304710 INFO @ Tue, 16 Jun 2020 09:17:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:17:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:17:32: #1 tags after filtering in treatment: 10325076 INFO @ Tue, 16 Jun 2020 09:17:32: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 09:17:32: #1 finished! INFO @ Tue, 16 Jun 2020 09:17:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:17:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:17:32: #2 number of paired peaks: 359 WARNING @ Tue, 16 Jun 2020 09:17:32: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Tue, 16 Jun 2020 09:17:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:17:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:17:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:17:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:17:32: #2 predicted fragment length is 136 bps INFO @ Tue, 16 Jun 2020 09:17:32: #2 alternative fragment length(s) may be 4,136 bps INFO @ Tue, 16 Jun 2020 09:17:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.05_model.r INFO @ Tue, 16 Jun 2020 09:17:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:17:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:17:33: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:17:38: 21000000 INFO @ Tue, 16 Jun 2020 09:17:40: 18000000 INFO @ Tue, 16 Jun 2020 09:17:46: 22000000 INFO @ Tue, 16 Jun 2020 09:17:46: 19000000 INFO @ Tue, 16 Jun 2020 09:17:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:53: 20000000 INFO @ Tue, 16 Jun 2020 09:17:54: 23000000 INFO @ Tue, 16 Jun 2020 09:18:00: 21000000 INFO @ Tue, 16 Jun 2020 09:18:02: 24000000 INFO @ Tue, 16 Jun 2020 09:18:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:18:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:18:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.05_summits.bed INFO @ Tue, 16 Jun 2020 09:18:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (453 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:18:07: 22000000 INFO @ Tue, 16 Jun 2020 09:18:10: 25000000 INFO @ Tue, 16 Jun 2020 09:18:14: 23000000 INFO @ Tue, 16 Jun 2020 09:18:17: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:18:17: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:18:17: #1 total tags in treatment: 11304710 INFO @ Tue, 16 Jun 2020 09:18:17: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:18:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:18:17: #1 tags after filtering in treatment: 10325076 INFO @ Tue, 16 Jun 2020 09:18:17: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 09:18:17: #1 finished! INFO @ Tue, 16 Jun 2020 09:18:17: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:18:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:18:18: #2 number of paired peaks: 359 WARNING @ Tue, 16 Jun 2020 09:18:18: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Tue, 16 Jun 2020 09:18:18: start model_add_line... INFO @ Tue, 16 Jun 2020 09:18:18: start X-correlation... INFO @ Tue, 16 Jun 2020 09:18:18: end of X-cor INFO @ Tue, 16 Jun 2020 09:18:18: #2 finished! INFO @ Tue, 16 Jun 2020 09:18:18: #2 predicted fragment length is 136 bps INFO @ Tue, 16 Jun 2020 09:18:18: #2 alternative fragment length(s) may be 4,136 bps INFO @ Tue, 16 Jun 2020 09:18:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.10_model.r INFO @ Tue, 16 Jun 2020 09:18:18: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:18:18: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:18:20: 24000000 INFO @ Tue, 16 Jun 2020 09:18:26: 25000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:18:32: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:18:32: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:18:32: #1 total tags in treatment: 11304710 INFO @ Tue, 16 Jun 2020 09:18:32: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:18:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:18:32: #1 tags after filtering in treatment: 10325076 INFO @ Tue, 16 Jun 2020 09:18:32: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 09:18:32: #1 finished! INFO @ Tue, 16 Jun 2020 09:18:32: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:18:32: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:18:33: #2 number of paired peaks: 359 WARNING @ Tue, 16 Jun 2020 09:18:33: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Tue, 16 Jun 2020 09:18:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:18:33: start X-correlation... INFO @ Tue, 16 Jun 2020 09:18:33: end of X-cor INFO @ Tue, 16 Jun 2020 09:18:33: #2 finished! INFO @ Tue, 16 Jun 2020 09:18:33: #2 predicted fragment length is 136 bps INFO @ Tue, 16 Jun 2020 09:18:33: #2 alternative fragment length(s) may be 4,136 bps INFO @ Tue, 16 Jun 2020 09:18:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.20_model.r INFO @ Tue, 16 Jun 2020 09:18:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:18:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:18:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:18:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:18:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:18:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.10_summits.bed INFO @ Tue, 16 Jun 2020 09:18:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (298 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:18:53: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:19:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:19:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:19:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085435/SRX4085435.20_summits.bed INFO @ Tue, 16 Jun 2020 09:19:03: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (192 records, 4 fields): 1 millis CompletedMACS2peakCalling