Job ID = 6367812 SRX = SRX4085380 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:36:14 prefetch.2.10.7: 1) Downloading 'SRR7167409'... 2020-06-15T23:36:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:41:15 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:41:15 prefetch.2.10.7: 1) 'SRR7167409' was downloaded successfully Read 12502185 spots for SRR7167409/SRR7167409.sra Written 12502185 spots for SRR7167409/SRR7167409.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: 00:06:11 12502185 reads; of these: 12502185 (100.00%) were paired; of these: 9150411 (73.19%) aligned concordantly 0 times 2942878 (23.54%) aligned concordantly exactly 1 time 408896 (3.27%) aligned concordantly >1 times ---- 9150411 pairs aligned concordantly 0 times; of these: 280561 (3.07%) aligned discordantly 1 time ---- 8869850 pairs aligned 0 times concordantly or discordantly; of these: 17739700 mates make up the pairs; of these: 12342934 (69.58%) aligned 0 times 4790408 (27.00%) aligned exactly 1 time 606358 (3.42%) aligned >1 times 50.64% overall alignment rate Time searching: 00:06:11 Overall time: 00:06:11 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] 211019 / 3491055 = 0.0604 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 08:52:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.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 08:52:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:52:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:52:36: 1000000 INFO @ Tue, 16 Jun 2020 08:52:43: 2000000 INFO @ Tue, 16 Jun 2020 08:52:49: 3000000 INFO @ Tue, 16 Jun 2020 08:52:56: 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 08:52:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.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 08:52:59: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:52:59: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:53:03: 5000000 INFO @ Tue, 16 Jun 2020 08:53:06: 1000000 INFO @ Tue, 16 Jun 2020 08:53:11: 6000000 INFO @ Tue, 16 Jun 2020 08:53:12: 2000000 INFO @ Tue, 16 Jun 2020 08:53:18: 7000000 INFO @ Tue, 16 Jun 2020 08:53:19: 3000000 INFO @ Tue, 16 Jun 2020 08:53:25: 4000000 INFO @ Tue, 16 Jun 2020 08:53:25: 8000000 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 08:53:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.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 08:53:29: #1 read tag files... INFO @ Tue, 16 Jun 2020 08:53:29: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 08:53:32: 5000000 INFO @ Tue, 16 Jun 2020 08:53:32: 9000000 INFO @ Tue, 16 Jun 2020 08:53:36: 1000000 INFO @ Tue, 16 Jun 2020 08:53:39: 6000000 INFO @ Tue, 16 Jun 2020 08:53:40: 10000000 INFO @ Tue, 16 Jun 2020 08:53:42: 2000000 INFO @ Tue, 16 Jun 2020 08:53:45: 7000000 INFO @ Tue, 16 Jun 2020 08:53:47: 11000000 INFO @ Tue, 16 Jun 2020 08:53:49: 3000000 INFO @ Tue, 16 Jun 2020 08:53:52: 8000000 INFO @ Tue, 16 Jun 2020 08:53:55: 12000000 INFO @ Tue, 16 Jun 2020 08:53:56: 4000000 INFO @ Tue, 16 Jun 2020 08:53:57: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:53:57: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:53:57: #1 total tags in treatment: 3148138 INFO @ Tue, 16 Jun 2020 08:53:57: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:53:57: #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 08:53:57: #1 tags after filtering in treatment: 2998446 INFO @ Tue, 16 Jun 2020 08:53:57: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 16 Jun 2020 08:53:57: #1 finished! INFO @ Tue, 16 Jun 2020 08:53:57: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:53:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:53:57: #2 number of paired peaks: 256 WARNING @ Tue, 16 Jun 2020 08:53:57: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Tue, 16 Jun 2020 08:53:57: start model_add_line... INFO @ Tue, 16 Jun 2020 08:53:57: start X-correlation... INFO @ Tue, 16 Jun 2020 08:53:57: end of X-cor INFO @ Tue, 16 Jun 2020 08:53:57: #2 finished! INFO @ Tue, 16 Jun 2020 08:53:57: #2 predicted fragment length is 165 bps INFO @ Tue, 16 Jun 2020 08:53:57: #2 alternative fragment length(s) may be 125,165,584 bps INFO @ Tue, 16 Jun 2020 08:53:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.05_model.r INFO @ Tue, 16 Jun 2020 08:53:57: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:53:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:53:58: 9000000 INFO @ Tue, 16 Jun 2020 08:54:02: 5000000 INFO @ Tue, 16 Jun 2020 08:54:04: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:54:05: 10000000 INFO @ Tue, 16 Jun 2020 08:54:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.05_peaks.xls INFO @ Tue, 16 Jun 2020 08:54:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:54:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.05_summits.bed INFO @ Tue, 16 Jun 2020 08:54:08: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (349 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:54:08: 6000000 INFO @ Tue, 16 Jun 2020 08:54:11: 11000000 INFO @ Tue, 16 Jun 2020 08:54:15: 7000000 INFO @ Tue, 16 Jun 2020 08:54:18: 12000000 INFO @ Tue, 16 Jun 2020 08:54:19: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:54:19: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:54:19: #1 total tags in treatment: 3148138 INFO @ Tue, 16 Jun 2020 08:54:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:54:19: #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 08:54:19: #1 tags after filtering in treatment: 2998446 INFO @ Tue, 16 Jun 2020 08:54:19: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 16 Jun 2020 08:54:19: #1 finished! INFO @ Tue, 16 Jun 2020 08:54:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:54:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:54:19: #2 number of paired peaks: 256 WARNING @ Tue, 16 Jun 2020 08:54:19: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Tue, 16 Jun 2020 08:54:19: start model_add_line... INFO @ Tue, 16 Jun 2020 08:54:19: start X-correlation... INFO @ Tue, 16 Jun 2020 08:54:19: end of X-cor INFO @ Tue, 16 Jun 2020 08:54:19: #2 finished! INFO @ Tue, 16 Jun 2020 08:54:19: #2 predicted fragment length is 165 bps INFO @ Tue, 16 Jun 2020 08:54:19: #2 alternative fragment length(s) may be 125,165,584 bps INFO @ Tue, 16 Jun 2020 08:54:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.10_model.r INFO @ Tue, 16 Jun 2020 08:54:19: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:54:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:54:21: 8000000 INFO @ Tue, 16 Jun 2020 08:54:26: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 08:54:27: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 08:54:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.10_peaks.xls INFO @ Tue, 16 Jun 2020 08:54:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:54:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.10_summits.bed INFO @ Tue, 16 Jun 2020 08:54:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (165 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 08:54:32: 10000000 INFO @ Tue, 16 Jun 2020 08:54:38: 11000000 INFO @ Tue, 16 Jun 2020 08:54:44: 12000000 INFO @ Tue, 16 Jun 2020 08:54:45: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 08:54:45: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 08:54:45: #1 total tags in treatment: 3148138 INFO @ Tue, 16 Jun 2020 08:54:45: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 08:54:45: #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 08:54:45: #1 tags after filtering in treatment: 2998446 INFO @ Tue, 16 Jun 2020 08:54:45: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 16 Jun 2020 08:54:45: #1 finished! INFO @ Tue, 16 Jun 2020 08:54:45: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 08:54:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 08:54:45: #2 number of paired peaks: 256 WARNING @ Tue, 16 Jun 2020 08:54:45: Fewer paired peaks (256) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 256 pairs to build model! INFO @ Tue, 16 Jun 2020 08:54:45: start model_add_line... INFO @ Tue, 16 Jun 2020 08:54:45: start X-correlation... INFO @ Tue, 16 Jun 2020 08:54:45: end of X-cor INFO @ Tue, 16 Jun 2020 08:54:45: #2 finished! INFO @ Tue, 16 Jun 2020 08:54:45: #2 predicted fragment length is 165 bps INFO @ Tue, 16 Jun 2020 08:54:45: #2 alternative fragment length(s) may be 125,165,584 bps INFO @ Tue, 16 Jun 2020 08:54:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.20_model.r INFO @ Tue, 16 Jun 2020 08:54:45: #3 Call peaks... INFO @ Tue, 16 Jun 2020 08:54:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 08:54:52: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 08:54:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.20_peaks.xls INFO @ Tue, 16 Jun 2020 08:54:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 08:54:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085380/SRX4085380.20_summits.bed INFO @ Tue, 16 Jun 2020 08:54:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (61 records, 4 fields): 1 millis CompletedMACS2peakCalling