Job ID = 6497392 SRX = SRX4085422 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-25T21:47:15 prefetch.2.10.7: 1) Downloading 'SRR7167451'... 2020-06-25T21:47:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T21:49:54 prefetch.2.10.7: HTTPS download succeed 2020-06-25T21:49:54 prefetch.2.10.7: 1) 'SRR7167451' was downloaded successfully Read 15275286 spots for SRR7167451/SRR7167451.sra Written 15275286 spots for SRR7167451/SRR7167451.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: 00:11:41 15275286 reads; of these: 15275286 (100.00%) were paired; of these: 8905404 (58.30%) aligned concordantly 0 times 5409515 (35.41%) aligned concordantly exactly 1 time 960367 (6.29%) aligned concordantly >1 times ---- 8905404 pairs aligned concordantly 0 times; of these: 324491 (3.64%) aligned discordantly 1 time ---- 8580913 pairs aligned 0 times concordantly or discordantly; of these: 17161826 mates make up the pairs; of these: 13034116 (75.95%) aligned 0 times 3681516 (21.45%) aligned exactly 1 time 446194 (2.60%) aligned >1 times 57.34% overall alignment rate Time searching: 00:11:41 Overall time: 00:11:41 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 8 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] 453838 / 6581356 = 0.0690 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 07:10:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.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 07:10:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:10:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:10:12: 1000000 INFO @ Fri, 26 Jun 2020 07:10:18: 2000000 INFO @ Fri, 26 Jun 2020 07:10:23: 3000000 INFO @ Fri, 26 Jun 2020 07:10:28: 4000000 INFO @ Fri, 26 Jun 2020 07:10:34: 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 @ Fri, 26 Jun 2020 07:10:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.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 07:10:37: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:10:37: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:10:39: 6000000 INFO @ Fri, 26 Jun 2020 07:10:43: 1000000 INFO @ Fri, 26 Jun 2020 07:10:45: 7000000 INFO @ Fri, 26 Jun 2020 07:10:49: 2000000 INFO @ Fri, 26 Jun 2020 07:10:51: 8000000 INFO @ Fri, 26 Jun 2020 07:10:55: 3000000 INFO @ Fri, 26 Jun 2020 07:10:57: 9000000 INFO @ Fri, 26 Jun 2020 07:11:01: 4000000 INFO @ Fri, 26 Jun 2020 07:11:03: 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 @ Fri, 26 Jun 2020 07:11:07: 5000000 INFO @ Fri, 26 Jun 2020 07:11:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.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 07:11:07: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:11:07: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:11:09: 11000000 INFO @ Fri, 26 Jun 2020 07:11:13: 6000000 INFO @ Fri, 26 Jun 2020 07:11:13: 1000000 INFO @ Fri, 26 Jun 2020 07:11:15: 12000000 INFO @ Fri, 26 Jun 2020 07:11:19: 7000000 INFO @ Fri, 26 Jun 2020 07:11:19: 2000000 INFO @ Fri, 26 Jun 2020 07:11:21: 13000000 INFO @ Fri, 26 Jun 2020 07:11:25: 8000000 INFO @ Fri, 26 Jun 2020 07:11:25: 3000000 INFO @ Fri, 26 Jun 2020 07:11:27: 14000000 INFO @ Fri, 26 Jun 2020 07:11:31: 9000000 INFO @ Fri, 26 Jun 2020 07:11:31: 4000000 INFO @ Fri, 26 Jun 2020 07:11:33: 15000000 INFO @ Fri, 26 Jun 2020 07:11:37: 10000000 INFO @ Fri, 26 Jun 2020 07:11:37: 5000000 INFO @ Fri, 26 Jun 2020 07:11:38: 16000000 INFO @ Fri, 26 Jun 2020 07:11:41: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:11:41: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:11:41: #1 total tags in treatment: 5927977 INFO @ Fri, 26 Jun 2020 07:11:41: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:11:41: #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 07:11:41: #1 tags after filtering in treatment: 5192531 INFO @ Fri, 26 Jun 2020 07:11:41: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 07:11:41: #1 finished! INFO @ Fri, 26 Jun 2020 07:11:41: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:11:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:11:42: #2 number of paired peaks: 546 WARNING @ Fri, 26 Jun 2020 07:11:42: Fewer paired peaks (546) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 546 pairs to build model! INFO @ Fri, 26 Jun 2020 07:11:42: start model_add_line... INFO @ Fri, 26 Jun 2020 07:11:42: start X-correlation... INFO @ Fri, 26 Jun 2020 07:11:42: end of X-cor INFO @ Fri, 26 Jun 2020 07:11:42: #2 finished! INFO @ Fri, 26 Jun 2020 07:11:42: #2 predicted fragment length is 87 bps INFO @ Fri, 26 Jun 2020 07:11:42: #2 alternative fragment length(s) may be 87 bps INFO @ Fri, 26 Jun 2020 07:11:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.05_model.r WARNING @ Fri, 26 Jun 2020 07:11:42: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:11:42: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Fri, 26 Jun 2020 07:11:42: #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 07:11:42: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:11:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:11:43: 11000000 INFO @ Fri, 26 Jun 2020 07:11:43: 6000000 INFO @ Fri, 26 Jun 2020 07:11:48: 12000000 INFO @ Fri, 26 Jun 2020 07:11:49: 7000000 INFO @ Fri, 26 Jun 2020 07:11:54: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:11:54: 13000000 INFO @ Fri, 26 Jun 2020 07:11:54: 8000000 INFO @ Fri, 26 Jun 2020 07:12:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:12:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:12:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.05_summits.bed INFO @ Fri, 26 Jun 2020 07:12:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3438 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:12:00: 14000000 INFO @ Fri, 26 Jun 2020 07:12:00: 9000000 INFO @ Fri, 26 Jun 2020 07:12:06: 15000000 INFO @ Fri, 26 Jun 2020 07:12:06: 10000000 INFO @ Fri, 26 Jun 2020 07:12:11: 16000000 INFO @ Fri, 26 Jun 2020 07:12:12: 11000000 INFO @ Fri, 26 Jun 2020 07:12:15: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:12:15: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:12:15: #1 total tags in treatment: 5927977 INFO @ Fri, 26 Jun 2020 07:12:15: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:12:15: #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 07:12:15: #1 tags after filtering in treatment: 5192531 INFO @ Fri, 26 Jun 2020 07:12:15: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 07:12:15: #1 finished! INFO @ Fri, 26 Jun 2020 07:12:15: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:12:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:12:15: #2 number of paired peaks: 546 WARNING @ Fri, 26 Jun 2020 07:12:15: Fewer paired peaks (546) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 546 pairs to build model! INFO @ Fri, 26 Jun 2020 07:12:15: start model_add_line... INFO @ Fri, 26 Jun 2020 07:12:15: start X-correlation... INFO @ Fri, 26 Jun 2020 07:12:15: end of X-cor INFO @ Fri, 26 Jun 2020 07:12:15: #2 finished! INFO @ Fri, 26 Jun 2020 07:12:15: #2 predicted fragment length is 87 bps INFO @ Fri, 26 Jun 2020 07:12:15: #2 alternative fragment length(s) may be 87 bps INFO @ Fri, 26 Jun 2020 07:12:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.10_model.r WARNING @ Fri, 26 Jun 2020 07:12:15: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:12:15: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Fri, 26 Jun 2020 07:12:15: #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 07:12:15: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:12:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:12:18: 12000000 INFO @ Fri, 26 Jun 2020 07:12:23: 13000000 INFO @ Fri, 26 Jun 2020 07:12:27: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:12:29: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:12:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:12:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:12:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.10_summits.bed INFO @ Fri, 26 Jun 2020 07:12:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1834 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 07:12:34: 15000000 INFO @ Fri, 26 Jun 2020 07:12:39: 16000000 INFO @ Fri, 26 Jun 2020 07:12:42: #1 tag size is determined as 51 bps INFO @ Fri, 26 Jun 2020 07:12:42: #1 tag size = 51 INFO @ Fri, 26 Jun 2020 07:12:42: #1 total tags in treatment: 5927977 INFO @ Fri, 26 Jun 2020 07:12:42: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:12:42: #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 07:12:42: #1 tags after filtering in treatment: 5192531 INFO @ Fri, 26 Jun 2020 07:12:42: #1 Redundant rate of treatment: 0.12 INFO @ Fri, 26 Jun 2020 07:12:42: #1 finished! INFO @ Fri, 26 Jun 2020 07:12:42: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:12:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:12:42: #2 number of paired peaks: 546 WARNING @ Fri, 26 Jun 2020 07:12:42: Fewer paired peaks (546) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 546 pairs to build model! INFO @ Fri, 26 Jun 2020 07:12:42: start model_add_line... INFO @ Fri, 26 Jun 2020 07:12:42: start X-correlation... INFO @ Fri, 26 Jun 2020 07:12:42: end of X-cor INFO @ Fri, 26 Jun 2020 07:12:42: #2 finished! INFO @ Fri, 26 Jun 2020 07:12:42: #2 predicted fragment length is 87 bps INFO @ Fri, 26 Jun 2020 07:12:42: #2 alternative fragment length(s) may be 87 bps INFO @ Fri, 26 Jun 2020 07:12:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.20_model.r WARNING @ Fri, 26 Jun 2020 07:12:42: #2 Since the d (87) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:12:42: #2 You may need to consider one of the other alternative d(s): 87 WARNING @ Fri, 26 Jun 2020 07:12:42: #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 07:12:42: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:12:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:12:54: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:13:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:13:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:13:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4085422/SRX4085422.20_summits.bed INFO @ Fri, 26 Jun 2020 07:13:00: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (618 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。