Job ID = 6507745 SRX = SRX2011723 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-26T14:06:42 prefetch.2.10.7: 1) Downloading 'SRR4017965'... 2020-06-26T14:06:42 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T14:10:56 prefetch.2.10.7: HTTPS download succeed 2020-06-26T14:10:56 prefetch.2.10.7: 1) 'SRR4017965' was downloaded successfully Read 11867230 spots for SRR4017965/SRR4017965.sra Written 11867230 spots for SRR4017965/SRR4017965.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: 00:19:14 11867230 reads; of these: 11867230 (100.00%) were paired; of these: 773822 (6.52%) aligned concordantly 0 times 9748681 (82.15%) aligned concordantly exactly 1 time 1344727 (11.33%) aligned concordantly >1 times ---- 773822 pairs aligned concordantly 0 times; of these: 448519 (57.96%) aligned discordantly 1 time ---- 325303 pairs aligned 0 times concordantly or discordantly; of these: 650606 mates make up the pairs; of these: 475048 (73.02%) aligned 0 times 63950 (9.83%) aligned exactly 1 time 111608 (17.15%) aligned >1 times 98.00% overall alignment rate Time searching: 00:19:15 Overall time: 00:19:15 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 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] 2361293 / 11495402 = 0.2054 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 @ Fri, 26 Jun 2020 23:43:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.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 @ Fri, 26 Jun 2020 23:43:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:43:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:43:51: 1000000 INFO @ Fri, 26 Jun 2020 23:43:58: 2000000 INFO @ Fri, 26 Jun 2020 23:44:05: 3000000 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 @ Fri, 26 Jun 2020 23:44:12: 4000000 INFO @ Fri, 26 Jun 2020 23:44:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.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 @ Fri, 26 Jun 2020 23:44:13: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:44:13: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:44:19: 5000000 INFO @ Fri, 26 Jun 2020 23:44:21: 1000000 INFO @ Fri, 26 Jun 2020 23:44:27: 6000000 INFO @ Fri, 26 Jun 2020 23:44:29: 2000000 INFO @ Fri, 26 Jun 2020 23:44:34: 7000000 INFO @ Fri, 26 Jun 2020 23:44:36: 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 @ Fri, 26 Jun 2020 23:44:42: 8000000 INFO @ Fri, 26 Jun 2020 23:44:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.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 @ Fri, 26 Jun 2020 23:44:43: #1 read tag files... INFO @ Fri, 26 Jun 2020 23:44:43: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 23:44:44: 4000000 INFO @ Fri, 26 Jun 2020 23:44:50: 9000000 INFO @ Fri, 26 Jun 2020 23:44:52: 1000000 INFO @ Fri, 26 Jun 2020 23:44:53: 5000000 INFO @ Fri, 26 Jun 2020 23:44:59: 10000000 INFO @ Fri, 26 Jun 2020 23:45:01: 2000000 INFO @ Fri, 26 Jun 2020 23:45:01: 6000000 INFO @ Fri, 26 Jun 2020 23:45:08: 11000000 INFO @ Fri, 26 Jun 2020 23:45:09: 3000000 INFO @ Fri, 26 Jun 2020 23:45:10: 7000000 INFO @ Fri, 26 Jun 2020 23:45:16: 12000000 INFO @ Fri, 26 Jun 2020 23:45:18: 4000000 INFO @ Fri, 26 Jun 2020 23:45:18: 8000000 INFO @ Fri, 26 Jun 2020 23:45:25: 13000000 INFO @ Fri, 26 Jun 2020 23:45:27: 5000000 INFO @ Fri, 26 Jun 2020 23:45:27: 9000000 INFO @ Fri, 26 Jun 2020 23:45:33: 14000000 INFO @ Fri, 26 Jun 2020 23:45:35: 6000000 INFO @ Fri, 26 Jun 2020 23:45:36: 10000000 INFO @ Fri, 26 Jun 2020 23:45:42: 15000000 INFO @ Fri, 26 Jun 2020 23:45:44: 7000000 INFO @ Fri, 26 Jun 2020 23:45:45: 11000000 INFO @ Fri, 26 Jun 2020 23:45:50: 16000000 INFO @ Fri, 26 Jun 2020 23:45:53: 8000000 INFO @ Fri, 26 Jun 2020 23:45:53: 12000000 INFO @ Fri, 26 Jun 2020 23:45:59: 17000000 INFO @ Fri, 26 Jun 2020 23:46:01: 13000000 INFO @ Fri, 26 Jun 2020 23:46:01: 9000000 INFO @ Fri, 26 Jun 2020 23:46:07: 18000000 INFO @ Fri, 26 Jun 2020 23:46:10: 14000000 INFO @ Fri, 26 Jun 2020 23:46:10: 10000000 INFO @ Fri, 26 Jun 2020 23:46:11: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 23:46:11: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 23:46:11: #1 total tags in treatment: 8798063 INFO @ Fri, 26 Jun 2020 23:46:11: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:46:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:46:12: #1 tags after filtering in treatment: 7947796 INFO @ Fri, 26 Jun 2020 23:46:12: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 26 Jun 2020 23:46:12: #1 finished! INFO @ Fri, 26 Jun 2020 23:46:12: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:46:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:46:12: #2 number of paired peaks: 2001 INFO @ Fri, 26 Jun 2020 23:46:12: start model_add_line... INFO @ Fri, 26 Jun 2020 23:46:12: start X-correlation... INFO @ Fri, 26 Jun 2020 23:46:12: end of X-cor INFO @ Fri, 26 Jun 2020 23:46:12: #2 finished! INFO @ Fri, 26 Jun 2020 23:46:12: #2 predicted fragment length is 171 bps INFO @ Fri, 26 Jun 2020 23:46:12: #2 alternative fragment length(s) may be 171 bps INFO @ Fri, 26 Jun 2020 23:46:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.05_model.r WARNING @ Fri, 26 Jun 2020 23:46:12: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:46:12: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Fri, 26 Jun 2020 23:46:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:46:12: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:46:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:46:17: 15000000 INFO @ Fri, 26 Jun 2020 23:46:18: 11000000 INFO @ Fri, 26 Jun 2020 23:46:24: 16000000 INFO @ Fri, 26 Jun 2020 23:46:25: 12000000 INFO @ Fri, 26 Jun 2020 23:46:32: 17000000 INFO @ Fri, 26 Jun 2020 23:46:34: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 23:46:34: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:46:39: 18000000 INFO @ Fri, 26 Jun 2020 23:46:42: 14000000 INFO @ Fri, 26 Jun 2020 23:46:43: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 23:46:43: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 23:46:43: #1 total tags in treatment: 8798063 INFO @ Fri, 26 Jun 2020 23:46:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:46:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:46:44: #1 tags after filtering in treatment: 7947796 INFO @ Fri, 26 Jun 2020 23:46:44: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 26 Jun 2020 23:46:44: #1 finished! INFO @ Fri, 26 Jun 2020 23:46:44: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:46:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:46:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.05_peaks.xls INFO @ Fri, 26 Jun 2020 23:46:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:46:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.05_summits.bed INFO @ Fri, 26 Jun 2020 23:46:44: Done! INFO @ Fri, 26 Jun 2020 23:46:44: #2 number of paired peaks: 2001 INFO @ Fri, 26 Jun 2020 23:46:44: start model_add_line... INFO @ Fri, 26 Jun 2020 23:46:44: start X-correlation... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4423 records, 4 fields): 7 millis INFO @ Fri, 26 Jun 2020 23:46:44: end of X-cor INFO @ Fri, 26 Jun 2020 23:46:44: #2 finished! INFO @ Fri, 26 Jun 2020 23:46:44: #2 predicted fragment length is 171 bps INFO @ Fri, 26 Jun 2020 23:46:44: #2 alternative fragment length(s) may be 171 bps INFO @ Fri, 26 Jun 2020 23:46:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.10_model.r WARNING @ Fri, 26 Jun 2020 23:46:44: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:46:44: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Fri, 26 Jun 2020 23:46:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:46:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:46:44: #3 Pre-compute pvalue-qvalue table... CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 23:46:49: 15000000 INFO @ Fri, 26 Jun 2020 23:46:56: 16000000 INFO @ Fri, 26 Jun 2020 23:47:02: 17000000 INFO @ Fri, 26 Jun 2020 23:47:06: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:47:09: 18000000 INFO @ Fri, 26 Jun 2020 23:47:13: #1 tag size is determined as 101 bps INFO @ Fri, 26 Jun 2020 23:47:13: #1 tag size = 101 INFO @ Fri, 26 Jun 2020 23:47:13: #1 total tags in treatment: 8798063 INFO @ Fri, 26 Jun 2020 23:47:13: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 23:47:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 23:47:13: #1 tags after filtering in treatment: 7947796 INFO @ Fri, 26 Jun 2020 23:47:13: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 26 Jun 2020 23:47:13: #1 finished! INFO @ Fri, 26 Jun 2020 23:47:13: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 23:47:13: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 23:47:14: #2 number of paired peaks: 2001 INFO @ Fri, 26 Jun 2020 23:47:14: start model_add_line... INFO @ Fri, 26 Jun 2020 23:47:14: start X-correlation... INFO @ Fri, 26 Jun 2020 23:47:14: end of X-cor INFO @ Fri, 26 Jun 2020 23:47:14: #2 finished! INFO @ Fri, 26 Jun 2020 23:47:14: #2 predicted fragment length is 171 bps INFO @ Fri, 26 Jun 2020 23:47:14: #2 alternative fragment length(s) may be 171 bps INFO @ Fri, 26 Jun 2020 23:47:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.20_model.r WARNING @ Fri, 26 Jun 2020 23:47:14: #2 Since the d (171) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 23:47:14: #2 You may need to consider one of the other alternative d(s): 171 WARNING @ Fri, 26 Jun 2020 23:47:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 23:47:14: #3 Call peaks... INFO @ Fri, 26 Jun 2020 23:47:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 23:47:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.10_peaks.xls INFO @ Fri, 26 Jun 2020 23:47:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:47:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.10_summits.bed INFO @ Fri, 26 Jun 2020 23:47:15: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2269 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 23:47:35: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 23:47:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.20_peaks.xls INFO @ Fri, 26 Jun 2020 23:47:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 23:47:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2011723/SRX2011723.20_summits.bed INFO @ Fri, 26 Jun 2020 23:47:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (875 records, 4 fields): 2 millis CompletedMACS2peakCalling