Job ID = 5720771 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 1,391,026 reads read : 2,782,052 reads written : 2,782,052 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:15 1391026 reads; of these: 1391026 (100.00%) were paired; of these: 171631 (12.34%) aligned concordantly 0 times 398722 (28.66%) aligned concordantly exactly 1 time 820673 (59.00%) aligned concordantly >1 times ---- 171631 pairs aligned concordantly 0 times; of these: 27813 (16.21%) aligned discordantly 1 time ---- 143818 pairs aligned 0 times concordantly or discordantly; of these: 287636 mates make up the pairs; of these: 136529 (47.47%) aligned 0 times 71952 (25.01%) aligned exactly 1 time 79155 (27.52%) aligned >1 times 95.09% overall alignment rate Time searching: 00:07:16 Overall time: 00:07:16 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 145684 / 1226155 = 0.1188 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 @ Thu, 16 Apr 2020 01:27:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 01:27:09: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:27:09: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:27:15: 1000000 INFO @ Thu, 16 Apr 2020 01:27:21: 2000000 INFO @ Thu, 16 Apr 2020 01:27:23: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 01:27:23: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 01:27:23: #1 total tags in treatment: 1074454 INFO @ Thu, 16 Apr 2020 01:27:23: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:27:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:27:23: #1 tags after filtering in treatment: 900857 INFO @ Thu, 16 Apr 2020 01:27:23: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 01:27:23: #1 finished! INFO @ Thu, 16 Apr 2020 01:27:23: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:27:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:27:23: #2 number of paired peaks: 3483 INFO @ Thu, 16 Apr 2020 01:27:23: start model_add_line... INFO @ Thu, 16 Apr 2020 01:27:23: start X-correlation... INFO @ Thu, 16 Apr 2020 01:27:23: end of X-cor INFO @ Thu, 16 Apr 2020 01:27:23: #2 finished! INFO @ Thu, 16 Apr 2020 01:27:23: #2 predicted fragment length is 135 bps INFO @ Thu, 16 Apr 2020 01:27:23: #2 alternative fragment length(s) may be 135 bps INFO @ Thu, 16 Apr 2020 01:27:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.05_model.r WARNING @ Thu, 16 Apr 2020 01:27:23: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:27:23: #2 You may need to consider one of the other alternative d(s): 135 WARNING @ Thu, 16 Apr 2020 01:27:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:27:23: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:27:23: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:27:25: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:27:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:27:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:27:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.05_summits.bed INFO @ Thu, 16 Apr 2020 01:27:26: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2191 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 @ Thu, 16 Apr 2020 01:27:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 01:27:39: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:27:39: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:27:48: 1000000 INFO @ Thu, 16 Apr 2020 01:27:56: 2000000 INFO @ Thu, 16 Apr 2020 01:27:58: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 01:27:58: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 01:27:58: #1 total tags in treatment: 1074454 INFO @ Thu, 16 Apr 2020 01:27:58: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:27:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:27:59: #1 tags after filtering in treatment: 900857 INFO @ Thu, 16 Apr 2020 01:27:59: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 01:27:59: #1 finished! INFO @ Thu, 16 Apr 2020 01:27:59: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:27:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:27:59: #2 number of paired peaks: 3483 INFO @ Thu, 16 Apr 2020 01:27:59: start model_add_line... INFO @ Thu, 16 Apr 2020 01:27:59: start X-correlation... INFO @ Thu, 16 Apr 2020 01:27:59: end of X-cor INFO @ Thu, 16 Apr 2020 01:27:59: #2 finished! INFO @ Thu, 16 Apr 2020 01:27:59: #2 predicted fragment length is 135 bps INFO @ Thu, 16 Apr 2020 01:27:59: #2 alternative fragment length(s) may be 135 bps INFO @ Thu, 16 Apr 2020 01:27:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.10_model.r WARNING @ Thu, 16 Apr 2020 01:27:59: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:27:59: #2 You may need to consider one of the other alternative d(s): 135 WARNING @ Thu, 16 Apr 2020 01:27:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:27:59: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:27:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:28:01: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:28:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:28:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:28:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.10_summits.bed INFO @ Thu, 16 Apr 2020 01:28:02: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1423 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 @ Thu, 16 Apr 2020 01:28:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 16 Apr 2020 01:28:09: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:28:09: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:28:17: 1000000 INFO @ Thu, 16 Apr 2020 01:28:25: 2000000 INFO @ Thu, 16 Apr 2020 01:28:27: #1 tag size is determined as 74 bps INFO @ Thu, 16 Apr 2020 01:28:27: #1 tag size = 74 INFO @ Thu, 16 Apr 2020 01:28:27: #1 total tags in treatment: 1074454 INFO @ Thu, 16 Apr 2020 01:28:27: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:28:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 01:28:28: #1 tags after filtering in treatment: 900857 INFO @ Thu, 16 Apr 2020 01:28:28: #1 Redundant rate of treatment: 0.16 INFO @ Thu, 16 Apr 2020 01:28:28: #1 finished! INFO @ Thu, 16 Apr 2020 01:28:28: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:28:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:28:28: #2 number of paired peaks: 3483 INFO @ Thu, 16 Apr 2020 01:28:28: start model_add_line... INFO @ Thu, 16 Apr 2020 01:28:28: start X-correlation... INFO @ Thu, 16 Apr 2020 01:28:28: end of X-cor INFO @ Thu, 16 Apr 2020 01:28:28: #2 finished! INFO @ Thu, 16 Apr 2020 01:28:28: #2 predicted fragment length is 135 bps INFO @ Thu, 16 Apr 2020 01:28:28: #2 alternative fragment length(s) may be 135 bps INFO @ Thu, 16 Apr 2020 01:28:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.20_model.r WARNING @ Thu, 16 Apr 2020 01:28:28: #2 Since the d (135) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:28:28: #2 You may need to consider one of the other alternative d(s): 135 WARNING @ Thu, 16 Apr 2020 01:28:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 01:28:28: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:28:28: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:28:30: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:28:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:28:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:28:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5227008/SRX5227008.20_summits.bed INFO @ Thu, 16 Apr 2020 01:28:31: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (890 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。