Job ID = 6367774 SRX = SRX4085344 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:40:14 prefetch.2.10.7: 1) Downloading 'SRR7167373'... 2020-06-15T23:40:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:34 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:34 prefetch.2.10.7: 1) 'SRR7167373' was downloaded successfully Read 15586363 spots for SRR7167373/SRR7167373.sra Written 15586363 spots for SRR7167373/SRR7167373.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: 00:12:32 15586363 reads; of these: 15586363 (100.00%) were paired; of these: 729346 (4.68%) aligned concordantly 0 times 13232848 (84.90%) aligned concordantly exactly 1 time 1624169 (10.42%) aligned concordantly >1 times ---- 729346 pairs aligned concordantly 0 times; of these: 144313 (19.79%) aligned discordantly 1 time ---- 585033 pairs aligned 0 times concordantly or discordantly; of these: 1170066 mates make up the pairs; of these: 627028 (53.59%) aligned 0 times 433555 (37.05%) aligned exactly 1 time 109483 (9.36%) aligned >1 times 97.99% overall alignment rate Time searching: 00:12:32 Overall time: 00:12:32 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 16 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] 1247392 / 14935203 = 0.0835 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 09:12:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.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 09:12:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:12:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:12:40: 1000000 INFO @ Tue, 16 Jun 2020 09:12:46: 2000000 INFO @ Tue, 16 Jun 2020 09:12:52: 3000000 INFO @ Tue, 16 Jun 2020 09:12:58: 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 09:13:03: 5000000 INFO @ Tue, 16 Jun 2020 09:13:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.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 09:13:04: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:04: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:09: 6000000 INFO @ Tue, 16 Jun 2020 09:13:11: 1000000 INFO @ Tue, 16 Jun 2020 09:13:16: 7000000 INFO @ Tue, 16 Jun 2020 09:13:17: 2000000 INFO @ Tue, 16 Jun 2020 09:13:22: 8000000 INFO @ Tue, 16 Jun 2020 09:13:23: 3000000 INFO @ Tue, 16 Jun 2020 09:13:28: 9000000 INFO @ Tue, 16 Jun 2020 09:13:30: 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 09:13:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.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 09:13:34: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:13:34: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:13:34: 10000000 INFO @ Tue, 16 Jun 2020 09:13:36: 5000000 INFO @ Tue, 16 Jun 2020 09:13:41: 1000000 INFO @ Tue, 16 Jun 2020 09:13:41: 11000000 INFO @ Tue, 16 Jun 2020 09:13:42: 6000000 INFO @ Tue, 16 Jun 2020 09:13:47: 2000000 INFO @ Tue, 16 Jun 2020 09:13:47: 12000000 INFO @ Tue, 16 Jun 2020 09:13:49: 7000000 INFO @ Tue, 16 Jun 2020 09:13:53: 3000000 INFO @ Tue, 16 Jun 2020 09:13:53: 13000000 INFO @ Tue, 16 Jun 2020 09:13:55: 8000000 INFO @ Tue, 16 Jun 2020 09:14:00: 4000000 INFO @ Tue, 16 Jun 2020 09:14:00: 14000000 INFO @ Tue, 16 Jun 2020 09:14:01: 9000000 INFO @ Tue, 16 Jun 2020 09:14:06: 5000000 INFO @ Tue, 16 Jun 2020 09:14:06: 15000000 INFO @ Tue, 16 Jun 2020 09:14:08: 10000000 INFO @ Tue, 16 Jun 2020 09:14:12: 6000000 INFO @ Tue, 16 Jun 2020 09:14:13: 16000000 INFO @ Tue, 16 Jun 2020 09:14:14: 11000000 INFO @ Tue, 16 Jun 2020 09:14:19: 7000000 INFO @ Tue, 16 Jun 2020 09:14:19: 17000000 INFO @ Tue, 16 Jun 2020 09:14:21: 12000000 INFO @ Tue, 16 Jun 2020 09:14:25: 8000000 INFO @ Tue, 16 Jun 2020 09:14:26: 18000000 INFO @ Tue, 16 Jun 2020 09:14:27: 13000000 INFO @ Tue, 16 Jun 2020 09:14:32: 9000000 INFO @ Tue, 16 Jun 2020 09:14:33: 19000000 INFO @ Tue, 16 Jun 2020 09:14:34: 14000000 INFO @ Tue, 16 Jun 2020 09:14:39: 10000000 INFO @ Tue, 16 Jun 2020 09:14:39: 20000000 INFO @ Tue, 16 Jun 2020 09:14:41: 15000000 INFO @ Tue, 16 Jun 2020 09:14:45: 11000000 INFO @ Tue, 16 Jun 2020 09:14:46: 21000000 INFO @ Tue, 16 Jun 2020 09:14:47: 16000000 INFO @ Tue, 16 Jun 2020 09:14:52: 12000000 INFO @ Tue, 16 Jun 2020 09:14:52: 22000000 INFO @ Tue, 16 Jun 2020 09:14:54: 17000000 INFO @ Tue, 16 Jun 2020 09:14:58: 13000000 INFO @ Tue, 16 Jun 2020 09:14:59: 23000000 INFO @ Tue, 16 Jun 2020 09:15:01: 18000000 INFO @ Tue, 16 Jun 2020 09:15:05: 14000000 INFO @ Tue, 16 Jun 2020 09:15:06: 24000000 INFO @ Tue, 16 Jun 2020 09:15:08: 19000000 INFO @ Tue, 16 Jun 2020 09:15:12: 15000000 INFO @ Tue, 16 Jun 2020 09:15:13: 25000000 INFO @ Tue, 16 Jun 2020 09:15:15: 20000000 INFO @ Tue, 16 Jun 2020 09:15:18: 16000000 INFO @ Tue, 16 Jun 2020 09:15:19: 26000000 INFO @ Tue, 16 Jun 2020 09:15:22: 21000000 INFO @ Tue, 16 Jun 2020 09:15:25: 17000000 INFO @ Tue, 16 Jun 2020 09:15:26: 27000000 INFO @ Tue, 16 Jun 2020 09:15:29: 22000000 INFO @ Tue, 16 Jun 2020 09:15:32: 18000000 INFO @ Tue, 16 Jun 2020 09:15:33: 28000000 INFO @ Tue, 16 Jun 2020 09:15:33: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:15:33: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:15:33: #1 total tags in treatment: 13613350 INFO @ Tue, 16 Jun 2020 09:15:33: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:15:33: #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 09:15:33: #1 tags after filtering in treatment: 12071665 INFO @ Tue, 16 Jun 2020 09:15:33: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 16 Jun 2020 09:15:33: #1 finished! INFO @ Tue, 16 Jun 2020 09:15:33: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:15:33: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:15:34: #2 number of paired peaks: 148 WARNING @ Tue, 16 Jun 2020 09:15:34: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 16 Jun 2020 09:15:34: start model_add_line... INFO @ Tue, 16 Jun 2020 09:15:34: start X-correlation... INFO @ Tue, 16 Jun 2020 09:15:34: end of X-cor INFO @ Tue, 16 Jun 2020 09:15:34: #2 finished! INFO @ Tue, 16 Jun 2020 09:15:34: #2 predicted fragment length is 97 bps INFO @ Tue, 16 Jun 2020 09:15:34: #2 alternative fragment length(s) may be 3,97,122,199,226 bps INFO @ Tue, 16 Jun 2020 09:15:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.05_model.r WARNING @ Tue, 16 Jun 2020 09:15:34: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:15:34: #2 You may need to consider one of the other alternative d(s): 3,97,122,199,226 WARNING @ Tue, 16 Jun 2020 09:15:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:15:34: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:15:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:15:36: 23000000 INFO @ Tue, 16 Jun 2020 09:15:38: 19000000 INFO @ Tue, 16 Jun 2020 09:15:43: 24000000 INFO @ Tue, 16 Jun 2020 09:15:45: 20000000 INFO @ Tue, 16 Jun 2020 09:15:49: 25000000 INFO @ Tue, 16 Jun 2020 09:15:51: 21000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:15:56: 26000000 INFO @ Tue, 16 Jun 2020 09:15:58: 22000000 INFO @ Tue, 16 Jun 2020 09:16:00: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:16:03: 27000000 INFO @ Tue, 16 Jun 2020 09:16:05: 23000000 INFO @ Tue, 16 Jun 2020 09:16:10: 28000000 INFO @ Tue, 16 Jun 2020 09:16:11: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:16:11: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:16:11: #1 total tags in treatment: 13613350 INFO @ Tue, 16 Jun 2020 09:16:11: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:11: #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 09:16:11: #1 tags after filtering in treatment: 12071665 INFO @ Tue, 16 Jun 2020 09:16:11: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 16 Jun 2020 09:16:11: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:11: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:11: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:11: 24000000 INFO @ Tue, 16 Jun 2020 09:16:12: #2 number of paired peaks: 148 WARNING @ Tue, 16 Jun 2020 09:16:12: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:12: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:12: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:12: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:12: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:12: #2 predicted fragment length is 97 bps INFO @ Tue, 16 Jun 2020 09:16:12: #2 alternative fragment length(s) may be 3,97,122,199,226 bps INFO @ Tue, 16 Jun 2020 09:16:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.10_model.r WARNING @ Tue, 16 Jun 2020 09:16:12: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:16:12: #2 You may need to consider one of the other alternative d(s): 3,97,122,199,226 WARNING @ Tue, 16 Jun 2020 09:16:12: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:16:12: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.05_summits.bed INFO @ Tue, 16 Jun 2020 09:16:13: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (2029 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:16:17: 25000000 INFO @ Tue, 16 Jun 2020 09:16:23: 26000000 INFO @ Tue, 16 Jun 2020 09:16:29: 27000000 INFO @ Tue, 16 Jun 2020 09:16:35: 28000000 INFO @ Tue, 16 Jun 2020 09:16:35: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:16:35: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:16:35: #1 total tags in treatment: 13613350 INFO @ Tue, 16 Jun 2020 09:16:35: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:16:35: #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 09:16:36: #1 tags after filtering in treatment: 12071665 INFO @ Tue, 16 Jun 2020 09:16:36: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 16 Jun 2020 09:16:36: #1 finished! INFO @ Tue, 16 Jun 2020 09:16:36: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:16:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:16:36: #2 number of paired peaks: 148 WARNING @ Tue, 16 Jun 2020 09:16:36: Fewer paired peaks (148) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 148 pairs to build model! INFO @ Tue, 16 Jun 2020 09:16:36: start model_add_line... INFO @ Tue, 16 Jun 2020 09:16:37: start X-correlation... INFO @ Tue, 16 Jun 2020 09:16:37: end of X-cor INFO @ Tue, 16 Jun 2020 09:16:37: #2 finished! INFO @ Tue, 16 Jun 2020 09:16:37: #2 predicted fragment length is 97 bps INFO @ Tue, 16 Jun 2020 09:16:37: #2 alternative fragment length(s) may be 3,97,122,199,226 bps INFO @ Tue, 16 Jun 2020 09:16:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.20_model.r WARNING @ Tue, 16 Jun 2020 09:16:37: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:16:37: #2 You may need to consider one of the other alternative d(s): 3,97,122,199,226 WARNING @ Tue, 16 Jun 2020 09:16:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:16:37: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:16:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:16:37: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:16:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:16:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:16:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.10_summits.bed INFO @ Tue, 16 Jun 2020 09:16:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (328 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:17:02: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:17:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:17:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:17:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085344/SRX4085344.20_summits.bed INFO @ Tue, 16 Jun 2020 09:17:15: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (107 records, 4 fields): 1 millis CompletedMACS2peakCalling