Job ID = 6367839 SRX = SRX4085407 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 'SRR7167436'... 2020-06-15T23:38:59 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:47:48 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:47:48 prefetch.2.10.7: 1) 'SRR7167436' was downloaded successfully Read 11435094 spots for SRR7167436/SRR7167436.sra Written 11435094 spots for SRR7167436/SRR7167436.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:07 11435094 reads; of these: 11435094 (100.00%) were paired; of these: 806089 (7.05%) aligned concordantly 0 times 9090685 (79.50%) aligned concordantly exactly 1 time 1538320 (13.45%) aligned concordantly >1 times ---- 806089 pairs aligned concordantly 0 times; of these: 279662 (34.69%) aligned discordantly 1 time ---- 526427 pairs aligned 0 times concordantly or discordantly; of these: 1052854 mates make up the pairs; of these: 522263 (49.60%) aligned 0 times 362833 (34.46%) aligned exactly 1 time 167758 (15.93%) aligned >1 times 97.72% overall alignment rate Time searching: 00:10:08 Overall time: 00:10:08 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] 2436985 / 10744974 = 0.2268 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 09:05:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.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 09:05:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:05:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:05:44: 1000000 INFO @ Tue, 16 Jun 2020 09:05:49: 2000000 INFO @ Tue, 16 Jun 2020 09:05:55: 3000000 INFO @ Tue, 16 Jun 2020 09:06:00: 4000000 INFO @ Tue, 16 Jun 2020 09:06:06: 5000000 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 09:06:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.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 09:06:09: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:09: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:11: 6000000 INFO @ Tue, 16 Jun 2020 09:06:14: 1000000 INFO @ Tue, 16 Jun 2020 09:06:17: 7000000 INFO @ Tue, 16 Jun 2020 09:06:20: 2000000 INFO @ Tue, 16 Jun 2020 09:06:22: 8000000 INFO @ Tue, 16 Jun 2020 09:06:26: 3000000 INFO @ Tue, 16 Jun 2020 09:06:28: 9000000 INFO @ Tue, 16 Jun 2020 09:06:32: 4000000 INFO @ Tue, 16 Jun 2020 09:06:34: 10000000 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 09:06:38: 5000000 INFO @ Tue, 16 Jun 2020 09:06:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.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 09:06:39: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:06:39: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:06:40: 11000000 INFO @ Tue, 16 Jun 2020 09:06:44: 6000000 INFO @ Tue, 16 Jun 2020 09:06:45: 1000000 INFO @ Tue, 16 Jun 2020 09:06:46: 12000000 INFO @ Tue, 16 Jun 2020 09:06:50: 7000000 INFO @ Tue, 16 Jun 2020 09:06:51: 2000000 INFO @ Tue, 16 Jun 2020 09:06:52: 13000000 INFO @ Tue, 16 Jun 2020 09:06:56: 8000000 INFO @ Tue, 16 Jun 2020 09:06:57: 3000000 INFO @ Tue, 16 Jun 2020 09:06:58: 14000000 INFO @ Tue, 16 Jun 2020 09:07:02: 9000000 INFO @ Tue, 16 Jun 2020 09:07:04: 4000000 INFO @ Tue, 16 Jun 2020 09:07:05: 15000000 INFO @ Tue, 16 Jun 2020 09:07:09: 10000000 INFO @ Tue, 16 Jun 2020 09:07:11: 5000000 INFO @ Tue, 16 Jun 2020 09:07:11: 16000000 INFO @ Tue, 16 Jun 2020 09:07:15: 11000000 INFO @ Tue, 16 Jun 2020 09:07:17: 6000000 INFO @ Tue, 16 Jun 2020 09:07:17: 17000000 INFO @ Tue, 16 Jun 2020 09:07:20: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:07:20: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:07:20: #1 total tags in treatment: 8214032 INFO @ Tue, 16 Jun 2020 09:07:20: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:07:20: #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 09:07:20: #1 tags after filtering in treatment: 7632038 INFO @ Tue, 16 Jun 2020 09:07:20: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 09:07:20: #1 finished! INFO @ Tue, 16 Jun 2020 09:07:20: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:07:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:07:21: #2 number of paired peaks: 318 WARNING @ Tue, 16 Jun 2020 09:07:21: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Tue, 16 Jun 2020 09:07:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:07:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:07:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:07:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:07:21: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 09:07:21: #2 alternative fragment length(s) may be 4,144 bps INFO @ Tue, 16 Jun 2020 09:07:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.05_model.r INFO @ Tue, 16 Jun 2020 09:07:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:07:21: 12000000 INFO @ Tue, 16 Jun 2020 09:07:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:07:23: 7000000 INFO @ Tue, 16 Jun 2020 09:07:27: 13000000 INFO @ Tue, 16 Jun 2020 09:07:30: 8000000 INFO @ Tue, 16 Jun 2020 09:07:33: 14000000 INFO @ Tue, 16 Jun 2020 09:07:36: 9000000 INFO @ Tue, 16 Jun 2020 09:07:38: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:07:40: 15000000 INFO @ Tue, 16 Jun 2020 09:07:43: 10000000 INFO @ Tue, 16 Jun 2020 09:07:46: 16000000 INFO @ Tue, 16 Jun 2020 09:07:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:07:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:07:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.05_summits.bed INFO @ Tue, 16 Jun 2020 09:07:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (276 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:07:49: 11000000 INFO @ Tue, 16 Jun 2020 09:07:52: 17000000 INFO @ Tue, 16 Jun 2020 09:07:55: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:07:55: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:07:55: #1 total tags in treatment: 8214032 INFO @ Tue, 16 Jun 2020 09:07:55: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:07:55: #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 09:07:55: #1 tags after filtering in treatment: 7632038 INFO @ Tue, 16 Jun 2020 09:07:55: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 09:07:55: #1 finished! INFO @ Tue, 16 Jun 2020 09:07:55: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:07:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:07:55: 12000000 INFO @ Tue, 16 Jun 2020 09:07:55: #2 number of paired peaks: 318 WARNING @ Tue, 16 Jun 2020 09:07:55: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Tue, 16 Jun 2020 09:07:55: start model_add_line... INFO @ Tue, 16 Jun 2020 09:07:55: start X-correlation... INFO @ Tue, 16 Jun 2020 09:07:55: end of X-cor INFO @ Tue, 16 Jun 2020 09:07:55: #2 finished! INFO @ Tue, 16 Jun 2020 09:07:55: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 09:07:55: #2 alternative fragment length(s) may be 4,144 bps INFO @ Tue, 16 Jun 2020 09:07:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.10_model.r INFO @ Tue, 16 Jun 2020 09:07:55: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:07:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:08:01: 13000000 INFO @ Tue, 16 Jun 2020 09:08:06: 14000000 INFO @ Tue, 16 Jun 2020 09:08:12: 15000000 INFO @ Tue, 16 Jun 2020 09:08:12: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:08:17: 16000000 INFO @ Tue, 16 Jun 2020 09:08:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:08:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:08:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.10_summits.bed INFO @ Tue, 16 Jun 2020 09:08:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (213 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:08:23: 17000000 INFO @ Tue, 16 Jun 2020 09:08:25: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:08:25: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:08:25: #1 total tags in treatment: 8214032 INFO @ Tue, 16 Jun 2020 09:08:25: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:08:25: #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 09:08:25: #1 tags after filtering in treatment: 7632038 INFO @ Tue, 16 Jun 2020 09:08:25: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 16 Jun 2020 09:08:25: #1 finished! INFO @ Tue, 16 Jun 2020 09:08:25: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:08:25: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:08:26: #2 number of paired peaks: 318 WARNING @ Tue, 16 Jun 2020 09:08:26: Fewer paired peaks (318) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 318 pairs to build model! INFO @ Tue, 16 Jun 2020 09:08:26: start model_add_line... INFO @ Tue, 16 Jun 2020 09:08:26: start X-correlation... INFO @ Tue, 16 Jun 2020 09:08:26: end of X-cor INFO @ Tue, 16 Jun 2020 09:08:26: #2 finished! INFO @ Tue, 16 Jun 2020 09:08:26: #2 predicted fragment length is 144 bps INFO @ Tue, 16 Jun 2020 09:08:26: #2 alternative fragment length(s) may be 4,144 bps INFO @ Tue, 16 Jun 2020 09:08:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.20_model.r INFO @ Tue, 16 Jun 2020 09:08:26: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:08:26: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:08:42: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:08:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:08:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:08:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085407/SRX4085407.20_summits.bed INFO @ Tue, 16 Jun 2020 09:08:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (139 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。