Job ID = 5721059 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 4,234,288 reads read : 8,468,576 reads written : 8,468,576 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: 00:16:49 4234288 reads; of these: 4234288 (100.00%) were paired; of these: 767099 (18.12%) aligned concordantly 0 times 2445472 (57.75%) aligned concordantly exactly 1 time 1021717 (24.13%) aligned concordantly >1 times ---- 767099 pairs aligned concordantly 0 times; of these: 426577 (55.61%) aligned discordantly 1 time ---- 340522 pairs aligned 0 times concordantly or discordantly; of these: 681044 mates make up the pairs; of these: 200020 (29.37%) aligned 0 times 135637 (19.92%) aligned exactly 1 time 345387 (50.71%) aligned >1 times 97.64% overall alignment rate Time searching: 00:16:49 Overall time: 00:16:50 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_sort_core] merging from 8 files... [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] 417555 / 3858100 = 0.1082 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 04:19:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.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 04:19:27: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:19:27: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:19:36: 1000000 INFO @ Thu, 16 Apr 2020 04:19:45: 2000000 INFO @ Thu, 16 Apr 2020 04:19:53: 3000000 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 04:19:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.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 04:19:57: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:19:57: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:20:03: 4000000 INFO @ Thu, 16 Apr 2020 04:20:08: 1000000 INFO @ Thu, 16 Apr 2020 04:20:13: 5000000 INFO @ Thu, 16 Apr 2020 04:20:18: 2000000 INFO @ Thu, 16 Apr 2020 04:20:23: 6000000 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 04:20:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.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 04:20:28: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:20:28: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:20:29: 3000000 INFO @ Thu, 16 Apr 2020 04:20:34: 7000000 INFO @ Thu, 16 Apr 2020 04:20:39: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 04:20:39: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 04:20:39: #1 total tags in treatment: 3073336 INFO @ Thu, 16 Apr 2020 04:20:39: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:20:39: #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 04:20:39: #1 tags after filtering in treatment: 2966312 INFO @ Thu, 16 Apr 2020 04:20:39: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 04:20:39: #1 finished! INFO @ Thu, 16 Apr 2020 04:20:39: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:20:39: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:20:40: #2 number of paired peaks: 1396 INFO @ Thu, 16 Apr 2020 04:20:40: start model_add_line... INFO @ Thu, 16 Apr 2020 04:20:40: start X-correlation... INFO @ Thu, 16 Apr 2020 04:20:40: end of X-cor INFO @ Thu, 16 Apr 2020 04:20:40: #2 finished! INFO @ Thu, 16 Apr 2020 04:20:40: #2 predicted fragment length is 237 bps INFO @ Thu, 16 Apr 2020 04:20:40: #2 alternative fragment length(s) may be 237 bps INFO @ Thu, 16 Apr 2020 04:20:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.05_model.r WARNING @ Thu, 16 Apr 2020 04:20:40: #2 Since the d (237) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:20:40: #2 You may need to consider one of the other alternative d(s): 237 WARNING @ Thu, 16 Apr 2020 04:20:40: #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 04:20:40: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:20:40: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:20:41: 1000000 INFO @ Thu, 16 Apr 2020 04:20:41: 4000000 INFO @ Thu, 16 Apr 2020 04:20:47: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:20:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.05_peaks.xls INFO @ Thu, 16 Apr 2020 04:20:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:20:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.05_summits.bed INFO @ Thu, 16 Apr 2020 04:20:51: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1140 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:20:53: 5000000 INFO @ Thu, 16 Apr 2020 04:20:54: 2000000 INFO @ Thu, 16 Apr 2020 04:21:04: 6000000 INFO @ Thu, 16 Apr 2020 04:21:08: 3000000 INFO @ Thu, 16 Apr 2020 04:21:16: 7000000 INFO @ Thu, 16 Apr 2020 04:21:21: 4000000 INFO @ Thu, 16 Apr 2020 04:21:21: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 04:21:21: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 04:21:21: #1 total tags in treatment: 3073336 INFO @ Thu, 16 Apr 2020 04:21:21: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:21:21: #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 04:21:21: #1 tags after filtering in treatment: 2966312 INFO @ Thu, 16 Apr 2020 04:21:21: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 04:21:21: #1 finished! INFO @ Thu, 16 Apr 2020 04:21:21: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:21:21: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:21:21: #2 number of paired peaks: 1396 INFO @ Thu, 16 Apr 2020 04:21:21: start model_add_line... INFO @ Thu, 16 Apr 2020 04:21:21: start X-correlation... INFO @ Thu, 16 Apr 2020 04:21:22: end of X-cor INFO @ Thu, 16 Apr 2020 04:21:22: #2 finished! INFO @ Thu, 16 Apr 2020 04:21:22: #2 predicted fragment length is 237 bps INFO @ Thu, 16 Apr 2020 04:21:22: #2 alternative fragment length(s) may be 237 bps INFO @ Thu, 16 Apr 2020 04:21:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.10_model.r WARNING @ Thu, 16 Apr 2020 04:21:22: #2 Since the d (237) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:21:22: #2 You may need to consider one of the other alternative d(s): 237 WARNING @ Thu, 16 Apr 2020 04:21:22: #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 04:21:22: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:21:22: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:21:29: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:21:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.10_peaks.xls INFO @ Thu, 16 Apr 2020 04:21:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:21:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.10_summits.bed INFO @ Thu, 16 Apr 2020 04:21:32: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (683 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:21:33: 5000000 INFO @ Thu, 16 Apr 2020 04:21:44: 6000000 INFO @ Thu, 16 Apr 2020 04:21:56: 7000000 INFO @ Thu, 16 Apr 2020 04:22:02: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 04:22:02: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 04:22:02: #1 total tags in treatment: 3073336 INFO @ Thu, 16 Apr 2020 04:22:02: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:22:02: #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 04:22:02: #1 tags after filtering in treatment: 2966312 INFO @ Thu, 16 Apr 2020 04:22:02: #1 Redundant rate of treatment: 0.03 INFO @ Thu, 16 Apr 2020 04:22:02: #1 finished! INFO @ Thu, 16 Apr 2020 04:22:02: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:22:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:22:02: #2 number of paired peaks: 1396 INFO @ Thu, 16 Apr 2020 04:22:02: start model_add_line... INFO @ Thu, 16 Apr 2020 04:22:02: start X-correlation... INFO @ Thu, 16 Apr 2020 04:22:02: end of X-cor INFO @ Thu, 16 Apr 2020 04:22:02: #2 finished! INFO @ Thu, 16 Apr 2020 04:22:02: #2 predicted fragment length is 237 bps INFO @ Thu, 16 Apr 2020 04:22:02: #2 alternative fragment length(s) may be 237 bps INFO @ Thu, 16 Apr 2020 04:22:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.20_model.r WARNING @ Thu, 16 Apr 2020 04:22:02: #2 Since the d (237) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:22:02: #2 You may need to consider one of the other alternative d(s): 237 WARNING @ Thu, 16 Apr 2020 04:22:02: #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 04:22:02: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:22:02: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 04:22:09: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:22:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.20_peaks.xls INFO @ Thu, 16 Apr 2020 04:22:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:22:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448057/SRX6448057.20_summits.bed INFO @ Thu, 16 Apr 2020 04:22:12: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (345 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。