Job ID = 6367850 SRX = SRX4085418 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:47:29 prefetch.2.10.7: 1) Downloading 'SRR7167447'... 2020-06-15T23:47:29 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:53:00 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:53:00 prefetch.2.10.7: 1) 'SRR7167447' was downloaded successfully Read 21026682 spots for SRR7167447/SRR7167447.sra Written 21026682 spots for SRR7167447/SRR7167447.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: 00:14:01 21026682 reads; of these: 21026682 (100.00%) were paired; of these: 9194035 (43.73%) aligned concordantly 0 times 10036410 (47.73%) aligned concordantly exactly 1 time 1796237 (8.54%) aligned concordantly >1 times ---- 9194035 pairs aligned concordantly 0 times; of these: 348046 (3.79%) aligned discordantly 1 time ---- 8845989 pairs aligned 0 times concordantly or discordantly; of these: 17691978 mates make up the pairs; of these: 13785957 (77.92%) aligned 0 times 3385642 (19.14%) aligned exactly 1 time 520379 (2.94%) aligned >1 times 67.22% overall alignment rate Time searching: 00:14:01 Overall time: 00:14:01 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] 807859 / 12064728 = 0.0670 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 09:18:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.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 09:18:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:16: 1000000 INFO @ Tue, 16 Jun 2020 09:18:21: 2000000 INFO @ Tue, 16 Jun 2020 09:18:26: 3000000 INFO @ Tue, 16 Jun 2020 09:18:31: 4000000 INFO @ Tue, 16 Jun 2020 09:18:36: 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 09:18:41: 6000000 INFO @ Tue, 16 Jun 2020 09:18:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.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 09:18:41: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:18:41: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:18:46: 7000000 INFO @ Tue, 16 Jun 2020 09:18:46: 1000000 INFO @ Tue, 16 Jun 2020 09:18:52: 8000000 INFO @ Tue, 16 Jun 2020 09:18:52: 2000000 INFO @ Tue, 16 Jun 2020 09:18:57: 3000000 INFO @ Tue, 16 Jun 2020 09:18:57: 9000000 INFO @ Tue, 16 Jun 2020 09:19:02: 10000000 INFO @ Tue, 16 Jun 2020 09:19:02: 4000000 INFO @ Tue, 16 Jun 2020 09:19:07: 11000000 INFO @ Tue, 16 Jun 2020 09:19:07: 5000000 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 09:19:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.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 09:19:11: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:19:11: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:19:12: 6000000 INFO @ Tue, 16 Jun 2020 09:19:12: 12000000 INFO @ Tue, 16 Jun 2020 09:19:17: 1000000 INFO @ Tue, 16 Jun 2020 09:19:18: 7000000 INFO @ Tue, 16 Jun 2020 09:19:18: 13000000 INFO @ Tue, 16 Jun 2020 09:19:23: 14000000 INFO @ Tue, 16 Jun 2020 09:19:23: 8000000 INFO @ Tue, 16 Jun 2020 09:19:23: 2000000 INFO @ Tue, 16 Jun 2020 09:19:28: 15000000 INFO @ Tue, 16 Jun 2020 09:19:28: 9000000 INFO @ Tue, 16 Jun 2020 09:19:29: 3000000 INFO @ Tue, 16 Jun 2020 09:19:34: 16000000 INFO @ Tue, 16 Jun 2020 09:19:34: 10000000 INFO @ Tue, 16 Jun 2020 09:19:35: 4000000 INFO @ Tue, 16 Jun 2020 09:19:39: 17000000 INFO @ Tue, 16 Jun 2020 09:19:39: 11000000 INFO @ Tue, 16 Jun 2020 09:19:41: 5000000 INFO @ Tue, 16 Jun 2020 09:19:44: 18000000 INFO @ Tue, 16 Jun 2020 09:19:45: 12000000 INFO @ Tue, 16 Jun 2020 09:19:47: 6000000 INFO @ Tue, 16 Jun 2020 09:19:50: 19000000 INFO @ Tue, 16 Jun 2020 09:19:50: 13000000 INFO @ Tue, 16 Jun 2020 09:19:53: 7000000 INFO @ Tue, 16 Jun 2020 09:19:55: 20000000 INFO @ Tue, 16 Jun 2020 09:19:56: 14000000 INFO @ Tue, 16 Jun 2020 09:19:59: 8000000 INFO @ Tue, 16 Jun 2020 09:20:01: 21000000 INFO @ Tue, 16 Jun 2020 09:20:01: 15000000 INFO @ Tue, 16 Jun 2020 09:20:05: 9000000 INFO @ Tue, 16 Jun 2020 09:20:06: 22000000 INFO @ Tue, 16 Jun 2020 09:20:06: 16000000 INFO @ Tue, 16 Jun 2020 09:20:11: 10000000 INFO @ Tue, 16 Jun 2020 09:20:12: 23000000 INFO @ Tue, 16 Jun 2020 09:20:12: 17000000 INFO @ Tue, 16 Jun 2020 09:20:17: 24000000 INFO @ Tue, 16 Jun 2020 09:20:17: 18000000 INFO @ Tue, 16 Jun 2020 09:20:17: 11000000 INFO @ Tue, 16 Jun 2020 09:20:22: 25000000 INFO @ Tue, 16 Jun 2020 09:20:22: 19000000 INFO @ Tue, 16 Jun 2020 09:20:23: 12000000 INFO @ Tue, 16 Jun 2020 09:20:27: 26000000 INFO @ Tue, 16 Jun 2020 09:20:28: 20000000 INFO @ Tue, 16 Jun 2020 09:20:29: 13000000 INFO @ Tue, 16 Jun 2020 09:20:31: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:20:31: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:20:31: #1 total tags in treatment: 11042236 INFO @ Tue, 16 Jun 2020 09:20:31: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:31: #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 09:20:31: #1 tags after filtering in treatment: 10091778 INFO @ Tue, 16 Jun 2020 09:20:31: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 09:20:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:32: #2 number of paired peaks: 319 WARNING @ Tue, 16 Jun 2020 09:20:32: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:32: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:32: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:32: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:32: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:32: #2 predicted fragment length is 136 bps INFO @ Tue, 16 Jun 2020 09:20:32: #2 alternative fragment length(s) may be 4,124,133,136 bps INFO @ Tue, 16 Jun 2020 09:20:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.05_model.r INFO @ Tue, 16 Jun 2020 09:20:32: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:32: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:33: 21000000 INFO @ Tue, 16 Jun 2020 09:20:35: 14000000 INFO @ Tue, 16 Jun 2020 09:20:38: 22000000 INFO @ Tue, 16 Jun 2020 09:20:41: 15000000 INFO @ Tue, 16 Jun 2020 09:20:44: 23000000 INFO @ Tue, 16 Jun 2020 09:20:47: 16000000 INFO @ Tue, 16 Jun 2020 09:20:49: 24000000 INFO @ Tue, 16 Jun 2020 09:20:53: 17000000 INFO @ Tue, 16 Jun 2020 09:20:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:54: 25000000 INFO @ Tue, 16 Jun 2020 09:20:59: 18000000 INFO @ Tue, 16 Jun 2020 09:21:00: 26000000 INFO @ Tue, 16 Jun 2020 09:21:03: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:21:03: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:21:03: #1 total tags in treatment: 11042236 INFO @ Tue, 16 Jun 2020 09:21:03: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:03: #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 09:21:03: #1 tags after filtering in treatment: 10091778 INFO @ Tue, 16 Jun 2020 09:21:03: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 09:21:03: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:03: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:03: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:04: #2 number of paired peaks: 319 WARNING @ Tue, 16 Jun 2020 09:21:04: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:04: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:04: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:04: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:04: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:04: #2 predicted fragment length is 136 bps INFO @ Tue, 16 Jun 2020 09:21:04: #2 alternative fragment length(s) may be 4,124,133,136 bps INFO @ Tue, 16 Jun 2020 09:21:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.10_model.r INFO @ Tue, 16 Jun 2020 09:21:04: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:21:05: 19000000 INFO @ Tue, 16 Jun 2020 09:21:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.05_summits.bed INFO @ Tue, 16 Jun 2020 09:21:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1149 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:21:11: 20000000 INFO @ Tue, 16 Jun 2020 09:21:17: 21000000 INFO @ Tue, 16 Jun 2020 09:21:23: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:21:27: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:29: 23000000 INFO @ Tue, 16 Jun 2020 09:21:34: 24000000 INFO @ Tue, 16 Jun 2020 09:21:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.10_summits.bed INFO @ Tue, 16 Jun 2020 09:21:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (616 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:21:40: 25000000 INFO @ Tue, 16 Jun 2020 09:21:46: 26000000 INFO @ Tue, 16 Jun 2020 09:21:50: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:21:50: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:21:50: #1 total tags in treatment: 11042236 INFO @ Tue, 16 Jun 2020 09:21:50: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:21:50: #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 09:21:50: #1 tags after filtering in treatment: 10091778 INFO @ Tue, 16 Jun 2020 09:21:50: #1 Redundant rate of treatment: 0.09 INFO @ Tue, 16 Jun 2020 09:21:50: #1 finished! INFO @ Tue, 16 Jun 2020 09:21:50: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:21:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:21:51: #2 number of paired peaks: 319 WARNING @ Tue, 16 Jun 2020 09:21:51: Fewer paired peaks (319) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 319 pairs to build model! INFO @ Tue, 16 Jun 2020 09:21:51: start model_add_line... INFO @ Tue, 16 Jun 2020 09:21:51: start X-correlation... INFO @ Tue, 16 Jun 2020 09:21:51: end of X-cor INFO @ Tue, 16 Jun 2020 09:21:51: #2 finished! INFO @ Tue, 16 Jun 2020 09:21:51: #2 predicted fragment length is 136 bps INFO @ Tue, 16 Jun 2020 09:21:51: #2 alternative fragment length(s) may be 4,124,133,136 bps INFO @ Tue, 16 Jun 2020 09:21:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.20_model.r INFO @ Tue, 16 Jun 2020 09:21:51: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:21:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:22:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:22:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:22:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:22:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085418/SRX4085418.20_summits.bed INFO @ Tue, 16 Jun 2020 09:22:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (294 records, 4 fields): 1 millis CompletedMACS2peakCalling