Job ID = 6367875 SRX = SRX4085442 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:41:44 prefetch.2.10.7: 1) Downloading 'SRR7167471'... 2020-06-15T23:41:44 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:50:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:50:06 prefetch.2.10.7: 1) 'SRR7167471' was downloaded successfully Read 16165751 spots for SRR7167471/SRR7167471.sra Written 16165751 spots for SRR7167471/SRR7167471.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: 00:09:15 16165751 reads; of these: 16165751 (100.00%) were paired; of these: 8553679 (52.91%) aligned concordantly 0 times 6572311 (40.66%) aligned concordantly exactly 1 time 1039761 (6.43%) aligned concordantly >1 times ---- 8553679 pairs aligned concordantly 0 times; of these: 264198 (3.09%) aligned discordantly 1 time ---- 8289481 pairs aligned 0 times concordantly or discordantly; of these: 16578962 mates make up the pairs; of these: 13221979 (79.75%) aligned 0 times 2886079 (17.41%) aligned exactly 1 time 470904 (2.84%) aligned >1 times 59.10% overall alignment rate Time searching: 00:09:15 Overall time: 00:09:15 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 8 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] 744416 / 7766307 = 0.0959 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 09:06:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.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 09:06:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:59: 1000000 INFO @ Tue, 16 Jun 2020 09:07:06: 2000000 INFO @ Tue, 16 Jun 2020 09:07:12: 3000000 INFO @ Tue, 16 Jun 2020 09:07:18: 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 09:07:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.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 09:07:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:24: 5000000 INFO @ Tue, 16 Jun 2020 09:07:29: 1000000 INFO @ Tue, 16 Jun 2020 09:07:31: 6000000 INFO @ Tue, 16 Jun 2020 09:07:35: 2000000 INFO @ Tue, 16 Jun 2020 09:07:38: 7000000 INFO @ Tue, 16 Jun 2020 09:07:41: 3000000 INFO @ Tue, 16 Jun 2020 09:07:45: 8000000 INFO @ Tue, 16 Jun 2020 09:07:47: 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 @ Tue, 16 Jun 2020 09:07:52: 9000000 INFO @ Tue, 16 Jun 2020 09:07:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.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 09:07:53: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:07:53: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:07:53: 5000000 INFO @ Tue, 16 Jun 2020 09:07:58: 10000000 INFO @ Tue, 16 Jun 2020 09:07:59: 1000000 INFO @ Tue, 16 Jun 2020 09:07:59: 6000000 INFO @ Tue, 16 Jun 2020 09:08:05: 2000000 INFO @ Tue, 16 Jun 2020 09:08:05: 7000000 INFO @ Tue, 16 Jun 2020 09:08:05: 11000000 INFO @ Tue, 16 Jun 2020 09:08:11: 3000000 INFO @ Tue, 16 Jun 2020 09:08:11: 8000000 INFO @ Tue, 16 Jun 2020 09:08:12: 12000000 INFO @ Tue, 16 Jun 2020 09:08:17: 9000000 INFO @ Tue, 16 Jun 2020 09:08:17: 4000000 INFO @ Tue, 16 Jun 2020 09:08:19: 13000000 INFO @ Tue, 16 Jun 2020 09:08:22: 10000000 INFO @ Tue, 16 Jun 2020 09:08:23: 5000000 INFO @ Tue, 16 Jun 2020 09:08:26: 14000000 INFO @ Tue, 16 Jun 2020 09:08:28: 11000000 INFO @ Tue, 16 Jun 2020 09:08:29: 6000000 INFO @ Tue, 16 Jun 2020 09:08:33: 15000000 INFO @ Tue, 16 Jun 2020 09:08:34: 12000000 INFO @ Tue, 16 Jun 2020 09:08:35: 7000000 INFO @ Tue, 16 Jun 2020 09:08:39: 16000000 INFO @ Tue, 16 Jun 2020 09:08:40: 13000000 INFO @ Tue, 16 Jun 2020 09:08:41: 8000000 INFO @ Tue, 16 Jun 2020 09:08:45: 17000000 INFO @ Tue, 16 Jun 2020 09:08:45: 14000000 INFO @ Tue, 16 Jun 2020 09:08:46: 9000000 INFO @ Tue, 16 Jun 2020 09:08:49: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:08:49: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:08:49: #1 total tags in treatment: 6882289 INFO @ Tue, 16 Jun 2020 09:08:49: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:08:49: #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 09:08:49: #1 tags after filtering in treatment: 6334905 INFO @ Tue, 16 Jun 2020 09:08:49: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 09:08:49: #1 finished! INFO @ Tue, 16 Jun 2020 09:08:49: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:08:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:08:50: #2 number of paired peaks: 286 WARNING @ Tue, 16 Jun 2020 09:08:50: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Tue, 16 Jun 2020 09:08:50: start model_add_line... INFO @ Tue, 16 Jun 2020 09:08:50: start X-correlation... INFO @ Tue, 16 Jun 2020 09:08:50: end of X-cor INFO @ Tue, 16 Jun 2020 09:08:50: #2 finished! INFO @ Tue, 16 Jun 2020 09:08:50: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 09:08:50: #2 alternative fragment length(s) may be 4,131,149 bps INFO @ Tue, 16 Jun 2020 09:08:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.05_model.r INFO @ Tue, 16 Jun 2020 09:08:50: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:08:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:08:51: 15000000 INFO @ Tue, 16 Jun 2020 09:08:52: 10000000 INFO @ Tue, 16 Jun 2020 09:08:57: 16000000 INFO @ Tue, 16 Jun 2020 09:08:58: 11000000 INFO @ Tue, 16 Jun 2020 09:09:02: 17000000 INFO @ Tue, 16 Jun 2020 09:09:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:09:03: 12000000 INFO @ Tue, 16 Jun 2020 09:09:06: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:09:06: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:09:06: #1 total tags in treatment: 6882289 INFO @ Tue, 16 Jun 2020 09:09:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:06: #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 09:09:06: #1 tags after filtering in treatment: 6334905 INFO @ Tue, 16 Jun 2020 09:09:06: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 09:09:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:06: #2 number of paired peaks: 286 WARNING @ Tue, 16 Jun 2020 09:09:06: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Tue, 16 Jun 2020 09:09:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:06: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 09:09:06: #2 alternative fragment length(s) may be 4,131,149 bps INFO @ Tue, 16 Jun 2020 09:09:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.10_model.r INFO @ Tue, 16 Jun 2020 09:09:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:09:09: 13000000 INFO @ Tue, 16 Jun 2020 09:09:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:09:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:09:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.05_summits.bed INFO @ Tue, 16 Jun 2020 09:09:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (270 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:09:14: 14000000 INFO @ Tue, 16 Jun 2020 09:09:19: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:09:19: 15000000 INFO @ Tue, 16 Jun 2020 09:09:24: 16000000 INFO @ Tue, 16 Jun 2020 09:09:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:09:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:09:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.10_summits.bed INFO @ Tue, 16 Jun 2020 09:09:25: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (191 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:09:29: 17000000 INFO @ Tue, 16 Jun 2020 09:09:33: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:09:33: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:09:33: #1 total tags in treatment: 6882289 INFO @ Tue, 16 Jun 2020 09:09:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:09:33: #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 09:09:33: #1 tags after filtering in treatment: 6334905 INFO @ Tue, 16 Jun 2020 09:09:33: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 16 Jun 2020 09:09:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:09:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:09:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:09:33: #2 number of paired peaks: 286 WARNING @ Tue, 16 Jun 2020 09:09:33: Fewer paired peaks (286) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 286 pairs to build model! INFO @ Tue, 16 Jun 2020 09:09:33: start model_add_line... INFO @ Tue, 16 Jun 2020 09:09:33: start X-correlation... INFO @ Tue, 16 Jun 2020 09:09:33: end of X-cor INFO @ Tue, 16 Jun 2020 09:09:33: #2 finished! INFO @ Tue, 16 Jun 2020 09:09:33: #2 predicted fragment length is 149 bps INFO @ Tue, 16 Jun 2020 09:09:33: #2 alternative fragment length(s) may be 4,131,149 bps INFO @ Tue, 16 Jun 2020 09:09:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.20_model.r INFO @ Tue, 16 Jun 2020 09:09:33: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:09:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:09:46: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:09:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:09:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:09:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085442/SRX4085442.20_summits.bed INFO @ Tue, 16 Jun 2020 09:09:52: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (113 records, 4 fields): 3 millis CompletedMACS2peakCalling