Job ID = 6367806 SRX = SRX4085374 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:38:14 prefetch.2.10.7: 1) Downloading 'SRR7167403'... 2020-06-15T23:38:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:43:06 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:43:06 prefetch.2.10.7: 1) 'SRR7167403' was downloaded successfully Read 15348796 spots for SRR7167403/SRR7167403.sra Written 15348796 spots for SRR7167403/SRR7167403.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: 00:09:39 15348796 reads; of these: 15348796 (100.00%) were paired; of these: 7048648 (45.92%) aligned concordantly 0 times 7034593 (45.83%) aligned concordantly exactly 1 time 1265555 (8.25%) aligned concordantly >1 times ---- 7048648 pairs aligned concordantly 0 times; of these: 398436 (5.65%) aligned discordantly 1 time ---- 6650212 pairs aligned 0 times concordantly or discordantly; of these: 13300424 mates make up the pairs; of these: 9426916 (70.88%) aligned 0 times 3360445 (25.27%) aligned exactly 1 time 513063 (3.86%) aligned >1 times 69.29% overall alignment rate Time searching: 00:09:39 Overall time: 00:09:39 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] 531626 / 8573127 = 0.0620 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 09:00:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.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 09:00:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:00:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:00: 1000000 INFO @ Tue, 16 Jun 2020 09:01:06: 2000000 INFO @ Tue, 16 Jun 2020 09:01:12: 3000000 INFO @ Tue, 16 Jun 2020 09:01:18: 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 09:01:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.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 09:01:23: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:23: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:24: 5000000 INFO @ Tue, 16 Jun 2020 09:01:30: 1000000 INFO @ Tue, 16 Jun 2020 09:01:31: 6000000 INFO @ Tue, 16 Jun 2020 09:01:37: 2000000 INFO @ Tue, 16 Jun 2020 09:01:38: 7000000 INFO @ Tue, 16 Jun 2020 09:01:44: 3000000 INFO @ Tue, 16 Jun 2020 09:01:44: 8000000 INFO @ Tue, 16 Jun 2020 09:01:51: 4000000 INFO @ Tue, 16 Jun 2020 09:01:51: 9000000 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 09:01:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.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 09:01:54: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:01:54: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:01:57: 10000000 INFO @ Tue, 16 Jun 2020 09:01:58: 5000000 INFO @ Tue, 16 Jun 2020 09:02:01: 1000000 INFO @ Tue, 16 Jun 2020 09:02:04: 11000000 INFO @ Tue, 16 Jun 2020 09:02:05: 6000000 INFO @ Tue, 16 Jun 2020 09:02:08: 2000000 INFO @ Tue, 16 Jun 2020 09:02:11: 12000000 INFO @ Tue, 16 Jun 2020 09:02:12: 7000000 INFO @ Tue, 16 Jun 2020 09:02:14: 3000000 INFO @ Tue, 16 Jun 2020 09:02:18: 13000000 INFO @ Tue, 16 Jun 2020 09:02:18: 8000000 INFO @ Tue, 16 Jun 2020 09:02:21: 4000000 INFO @ Tue, 16 Jun 2020 09:02:25: 14000000 INFO @ Tue, 16 Jun 2020 09:02:25: 9000000 INFO @ Tue, 16 Jun 2020 09:02:28: 5000000 INFO @ Tue, 16 Jun 2020 09:02:32: 15000000 INFO @ Tue, 16 Jun 2020 09:02:32: 10000000 INFO @ Tue, 16 Jun 2020 09:02:35: 6000000 INFO @ Tue, 16 Jun 2020 09:02:38: 16000000 INFO @ Tue, 16 Jun 2020 09:02:39: 11000000 INFO @ Tue, 16 Jun 2020 09:02:41: 7000000 INFO @ Tue, 16 Jun 2020 09:02:45: 17000000 INFO @ Tue, 16 Jun 2020 09:02:46: 12000000 INFO @ Tue, 16 Jun 2020 09:02:48: 8000000 INFO @ Tue, 16 Jun 2020 09:02:52: 18000000 INFO @ Tue, 16 Jun 2020 09:02:52: 13000000 INFO @ Tue, 16 Jun 2020 09:02:55: 9000000 INFO @ Tue, 16 Jun 2020 09:02:58: 19000000 INFO @ Tue, 16 Jun 2020 09:02:59: 14000000 INFO @ Tue, 16 Jun 2020 09:03:01: 10000000 INFO @ Tue, 16 Jun 2020 09:03:05: 20000000 INFO @ Tue, 16 Jun 2020 09:03:06: 15000000 INFO @ Tue, 16 Jun 2020 09:03:06: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:03:06: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:03:06: #1 total tags in treatment: 7786972 INFO @ Tue, 16 Jun 2020 09:03:06: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:03:06: #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 09:03:06: #1 tags after filtering in treatment: 6918550 INFO @ Tue, 16 Jun 2020 09:03:06: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 16 Jun 2020 09:03:06: #1 finished! INFO @ Tue, 16 Jun 2020 09:03:06: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:03:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:03:06: #2 number of paired peaks: 472 WARNING @ Tue, 16 Jun 2020 09:03:06: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Tue, 16 Jun 2020 09:03:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:07: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:07: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:07: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:07: #2 predicted fragment length is 88 bps INFO @ Tue, 16 Jun 2020 09:03:07: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 16 Jun 2020 09:03:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.05_model.r WARNING @ Tue, 16 Jun 2020 09:03:07: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:03:07: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Tue, 16 Jun 2020 09:03:07: #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 09:03:07: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:07: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:03:08: 11000000 INFO @ Tue, 16 Jun 2020 09:03:12: 16000000 INFO @ Tue, 16 Jun 2020 09:03:14: 12000000 INFO @ Tue, 16 Jun 2020 09:03:19: 17000000 INFO @ Tue, 16 Jun 2020 09:03:21: 13000000 INFO @ Tue, 16 Jun 2020 09:03:24: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:03:25: 18000000 INFO @ Tue, 16 Jun 2020 09:03:27: 14000000 INFO @ Tue, 16 Jun 2020 09:03:32: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:03:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:03:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:03:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.05_summits.bed INFO @ Tue, 16 Jun 2020 09:03:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2860 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:03:34: 15000000 INFO @ Tue, 16 Jun 2020 09:03:38: 20000000 INFO @ Tue, 16 Jun 2020 09:03:39: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:03:39: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:03:39: #1 total tags in treatment: 7786972 INFO @ Tue, 16 Jun 2020 09:03:39: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:03:39: #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 09:03:39: #1 tags after filtering in treatment: 6918550 INFO @ Tue, 16 Jun 2020 09:03:39: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 16 Jun 2020 09:03:39: #1 finished! INFO @ Tue, 16 Jun 2020 09:03:39: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:03:39: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:03:40: #2 number of paired peaks: 472 WARNING @ Tue, 16 Jun 2020 09:03:40: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Tue, 16 Jun 2020 09:03:40: start model_add_line... INFO @ Tue, 16 Jun 2020 09:03:40: start X-correlation... INFO @ Tue, 16 Jun 2020 09:03:40: end of X-cor INFO @ Tue, 16 Jun 2020 09:03:40: #2 finished! INFO @ Tue, 16 Jun 2020 09:03:40: #2 predicted fragment length is 88 bps INFO @ Tue, 16 Jun 2020 09:03:40: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 16 Jun 2020 09:03:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.10_model.r WARNING @ Tue, 16 Jun 2020 09:03:40: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:03:40: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Tue, 16 Jun 2020 09:03:40: #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 09:03:40: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:03:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:03:40: 16000000 INFO @ Tue, 16 Jun 2020 09:03:46: 17000000 INFO @ Tue, 16 Jun 2020 09:03:52: 18000000 INFO @ Tue, 16 Jun 2020 09:03:56: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:03:58: 19000000 INFO @ Tue, 16 Jun 2020 09:04:04: 20000000 INFO @ Tue, 16 Jun 2020 09:04:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:04:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:04:05: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:04:05: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:04:05: #1 total tags in treatment: 7786972 INFO @ Tue, 16 Jun 2020 09:04:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:04:05: #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 09:04:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.10_summits.bed INFO @ Tue, 16 Jun 2020 09:04:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1658 records, 4 fields): 3 millis INFO @ Tue, 16 Jun 2020 09:04:05: #1 tags after filtering in treatment: 6918550 INFO @ Tue, 16 Jun 2020 09:04:05: #1 Redundant rate of treatment: 0.11 INFO @ Tue, 16 Jun 2020 09:04:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:04:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:04:05: #2 looking for paired plus/minus strand peaks... CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:04:05: #2 number of paired peaks: 472 WARNING @ Tue, 16 Jun 2020 09:04:05: Fewer paired peaks (472) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 472 pairs to build model! INFO @ Tue, 16 Jun 2020 09:04:05: start model_add_line... INFO @ Tue, 16 Jun 2020 09:04:05: start X-correlation... INFO @ Tue, 16 Jun 2020 09:04:05: end of X-cor INFO @ Tue, 16 Jun 2020 09:04:05: #2 finished! INFO @ Tue, 16 Jun 2020 09:04:05: #2 predicted fragment length is 88 bps INFO @ Tue, 16 Jun 2020 09:04:05: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 16 Jun 2020 09:04:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.20_model.r WARNING @ Tue, 16 Jun 2020 09:04:05: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:04:05: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Tue, 16 Jun 2020 09:04:05: #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 09:04:05: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:04:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:04:21: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:04:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:04:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:04:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085374/SRX4085374.20_summits.bed INFO @ Tue, 16 Jun 2020 09:04:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (775 records, 4 fields): 2 millis CompletedMACS2peakCalling