Job ID = 5790789 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,959,144 reads read : 13,918,288 reads written : 6,959,144 reads 0-length : 6,959,144 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:04:51 6959144 reads; of these: 6959144 (100.00%) were unpaired; of these: 199605 (2.87%) aligned 0 times 5051835 (72.59%) aligned exactly 1 time 1707704 (24.54%) aligned >1 times 97.13% overall alignment rate Time searching: 00:04:55 Overall time: 00:04:55 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 856200 / 6759539 = 0.1267 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 @ Wed, 22 Apr 2020 07:27:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 07:27:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:27:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:27:26: 1000000 INFO @ Wed, 22 Apr 2020 07:27:33: 2000000 INFO @ Wed, 22 Apr 2020 07:27:39: 3000000 INFO @ Wed, 22 Apr 2020 07:27:45: 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 @ Wed, 22 Apr 2020 07:27:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 07:27:50: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:27:50: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:27:52: 5000000 INFO @ Wed, 22 Apr 2020 07:27:57: 1000000 INFO @ Wed, 22 Apr 2020 07:27:59: #1 tag size is determined as 69 bps INFO @ Wed, 22 Apr 2020 07:27:59: #1 tag size = 69 INFO @ Wed, 22 Apr 2020 07:27:59: #1 total tags in treatment: 5903339 INFO @ Wed, 22 Apr 2020 07:27:59: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:27:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:27:59: #1 tags after filtering in treatment: 5903043 INFO @ Wed, 22 Apr 2020 07:27:59: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:27:59: #1 finished! INFO @ Wed, 22 Apr 2020 07:27:59: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:27:59: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:28:00: #2 number of paired peaks: 8982 INFO @ Wed, 22 Apr 2020 07:28:00: start model_add_line... INFO @ Wed, 22 Apr 2020 07:28:00: start X-correlation... INFO @ Wed, 22 Apr 2020 07:28:01: end of X-cor INFO @ Wed, 22 Apr 2020 07:28:01: #2 finished! INFO @ Wed, 22 Apr 2020 07:28:01: #2 predicted fragment length is 76 bps INFO @ Wed, 22 Apr 2020 07:28:01: #2 alternative fragment length(s) may be 76,172,199 bps INFO @ Wed, 22 Apr 2020 07:28:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.05_model.r WARNING @ Wed, 22 Apr 2020 07:28:01: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:28:01: #2 You may need to consider one of the other alternative d(s): 76,172,199 WARNING @ Wed, 22 Apr 2020 07:28:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:28:01: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:28:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:28:04: 2000000 INFO @ Wed, 22 Apr 2020 07:28:10: 3000000 INFO @ Wed, 22 Apr 2020 07:28:14: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:28:17: 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 @ Wed, 22 Apr 2020 07:28:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Wed, 22 Apr 2020 07:28:20: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:28:20: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:28:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:28:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:28:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.05_summits.bed INFO @ Wed, 22 Apr 2020 07:28:20: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (463 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:28:24: 5000000 INFO @ Wed, 22 Apr 2020 07:28:27: 1000000 INFO @ Wed, 22 Apr 2020 07:28:30: #1 tag size is determined as 69 bps INFO @ Wed, 22 Apr 2020 07:28:30: #1 tag size = 69 INFO @ Wed, 22 Apr 2020 07:28:30: #1 total tags in treatment: 5903339 INFO @ Wed, 22 Apr 2020 07:28:30: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:28:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:28:31: #1 tags after filtering in treatment: 5903043 INFO @ Wed, 22 Apr 2020 07:28:31: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:28:31: #1 finished! INFO @ Wed, 22 Apr 2020 07:28:31: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:28:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:28:32: #2 number of paired peaks: 8982 INFO @ Wed, 22 Apr 2020 07:28:32: start model_add_line... INFO @ Wed, 22 Apr 2020 07:28:32: start X-correlation... INFO @ Wed, 22 Apr 2020 07:28:32: end of X-cor INFO @ Wed, 22 Apr 2020 07:28:32: #2 finished! INFO @ Wed, 22 Apr 2020 07:28:32: #2 predicted fragment length is 76 bps INFO @ Wed, 22 Apr 2020 07:28:32: #2 alternative fragment length(s) may be 76,172,199 bps INFO @ Wed, 22 Apr 2020 07:28:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.10_model.r WARNING @ Wed, 22 Apr 2020 07:28:32: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:28:32: #2 You may need to consider one of the other alternative d(s): 76,172,199 WARNING @ Wed, 22 Apr 2020 07:28:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:28:32: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:28:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:28:34: 2000000 INFO @ Wed, 22 Apr 2020 07:28:41: 3000000 INFO @ Wed, 22 Apr 2020 07:28:46: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:28:47: 4000000 INFO @ Wed, 22 Apr 2020 07:28:52: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:28:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:28:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.10_summits.bed INFO @ Wed, 22 Apr 2020 07:28:52: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (280 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:28:54: 5000000 INFO @ Wed, 22 Apr 2020 07:28:59: #1 tag size is determined as 69 bps INFO @ Wed, 22 Apr 2020 07:28:59: #1 tag size = 69 INFO @ Wed, 22 Apr 2020 07:28:59: #1 total tags in treatment: 5903339 INFO @ Wed, 22 Apr 2020 07:28:59: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:28:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 07:29:00: #1 tags after filtering in treatment: 5903043 INFO @ Wed, 22 Apr 2020 07:29:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:29:00: #1 finished! INFO @ Wed, 22 Apr 2020 07:29:00: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:29:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:29:01: #2 number of paired peaks: 8982 INFO @ Wed, 22 Apr 2020 07:29:01: start model_add_line... INFO @ Wed, 22 Apr 2020 07:29:01: start X-correlation... INFO @ Wed, 22 Apr 2020 07:29:01: end of X-cor INFO @ Wed, 22 Apr 2020 07:29:01: #2 finished! INFO @ Wed, 22 Apr 2020 07:29:01: #2 predicted fragment length is 76 bps INFO @ Wed, 22 Apr 2020 07:29:01: #2 alternative fragment length(s) may be 76,172,199 bps INFO @ Wed, 22 Apr 2020 07:29:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.20_model.r WARNING @ Wed, 22 Apr 2020 07:29:01: #2 Since the d (76) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:29:01: #2 You may need to consider one of the other alternative d(s): 76,172,199 WARNING @ Wed, 22 Apr 2020 07:29:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 07:29:01: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:29:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:29:14: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:29:21: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:29:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:29:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625159/SRX7625159.20_summits.bed INFO @ Wed, 22 Apr 2020 07:29:21: Done! pass1 - making usageList (21 chroms): 1 millis pass2 - checking and writing primary data (142 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。