Job ID = 5721061 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 3,832,382 reads read : 7,664,764 reads written : 7,664,764 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:50 3832382 reads; of these: 3832382 (100.00%) were paired; of these: 374340 (9.77%) aligned concordantly 0 times 2384904 (62.23%) aligned concordantly exactly 1 time 1073138 (28.00%) aligned concordantly >1 times ---- 374340 pairs aligned concordantly 0 times; of these: 174510 (46.62%) aligned discordantly 1 time ---- 199830 pairs aligned 0 times concordantly or discordantly; of these: 399660 mates make up the pairs; of these: 167797 (41.98%) aligned 0 times 59641 (14.92%) aligned exactly 1 time 172222 (43.09%) aligned >1 times 97.81% overall alignment rate Time searching: 00:14:51 Overall time: 00:14:51 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] 437469 / 3577525 = 0.1223 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 04:17:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.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 04:17:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:17:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:17:24: 1000000 INFO @ Thu, 16 Apr 2020 04:17:31: 2000000 INFO @ Thu, 16 Apr 2020 04:17:38: 3000000 INFO @ Thu, 16 Apr 2020 04:17:44: 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 @ Thu, 16 Apr 2020 04:17:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.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 04:17:48: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:17:48: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:17:51: 5000000 INFO @ Thu, 16 Apr 2020 04:17:55: 1000000 INFO @ Thu, 16 Apr 2020 04:17:58: 6000000 INFO @ Thu, 16 Apr 2020 04:18:02: 2000000 INFO @ Thu, 16 Apr 2020 04:18:03: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 04:18:03: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 04:18:03: #1 total tags in treatment: 3035259 INFO @ Thu, 16 Apr 2020 04:18:03: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:18:03: #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 04:18:03: #1 tags after filtering in treatment: 2922604 INFO @ Thu, 16 Apr 2020 04:18:03: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 04:18:03: #1 finished! INFO @ Thu, 16 Apr 2020 04:18:03: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:18:03: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:18:03: #2 number of paired peaks: 1097 INFO @ Thu, 16 Apr 2020 04:18:03: start model_add_line... INFO @ Thu, 16 Apr 2020 04:18:03: start X-correlation... INFO @ Thu, 16 Apr 2020 04:18:03: end of X-cor INFO @ Thu, 16 Apr 2020 04:18:03: #2 finished! INFO @ Thu, 16 Apr 2020 04:18:03: #2 predicted fragment length is 188 bps INFO @ Thu, 16 Apr 2020 04:18:03: #2 alternative fragment length(s) may be 188 bps INFO @ Thu, 16 Apr 2020 04:18:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.05_model.r WARNING @ Thu, 16 Apr 2020 04:18:03: #2 Since the d (188) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:18:03: #2 You may need to consider one of the other alternative d(s): 188 WARNING @ Thu, 16 Apr 2020 04:18:03: #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 04:18:03: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:18:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:18:09: 3000000 INFO @ Thu, 16 Apr 2020 04:18:09: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:18:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.05_peaks.xls INFO @ Thu, 16 Apr 2020 04:18:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:18:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.05_summits.bed INFO @ Thu, 16 Apr 2020 04:18:13: Done! 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 pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (1247 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:18:16: 4000000 INFO @ Thu, 16 Apr 2020 04:18:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.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 04:18:18: #1 read tag files... INFO @ Thu, 16 Apr 2020 04:18:18: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 04:18:23: 5000000 INFO @ Thu, 16 Apr 2020 04:18:25: 1000000 INFO @ Thu, 16 Apr 2020 04:18:30: 6000000 INFO @ Thu, 16 Apr 2020 04:18:32: 2000000 INFO @ Thu, 16 Apr 2020 04:18:35: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 04:18:35: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 04:18:35: #1 total tags in treatment: 3035259 INFO @ Thu, 16 Apr 2020 04:18:35: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:18:35: #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 04:18:35: #1 tags after filtering in treatment: 2922604 INFO @ Thu, 16 Apr 2020 04:18:35: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 04:18:35: #1 finished! INFO @ Thu, 16 Apr 2020 04:18:35: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:18:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:18:35: #2 number of paired peaks: 1097 INFO @ Thu, 16 Apr 2020 04:18:35: start model_add_line... INFO @ Thu, 16 Apr 2020 04:18:35: start X-correlation... INFO @ Thu, 16 Apr 2020 04:18:35: end of X-cor INFO @ Thu, 16 Apr 2020 04:18:35: #2 finished! INFO @ Thu, 16 Apr 2020 04:18:35: #2 predicted fragment length is 188 bps INFO @ Thu, 16 Apr 2020 04:18:35: #2 alternative fragment length(s) may be 188 bps INFO @ Thu, 16 Apr 2020 04:18:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.10_model.r WARNING @ Thu, 16 Apr 2020 04:18:35: #2 Since the d (188) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:18:35: #2 You may need to consider one of the other alternative d(s): 188 WARNING @ Thu, 16 Apr 2020 04:18:35: #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 04:18:35: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:18:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:18:39: 3000000 INFO @ Thu, 16 Apr 2020 04:18:42: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:18:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.10_peaks.xls INFO @ Thu, 16 Apr 2020 04:18:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:18:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.10_summits.bed INFO @ Thu, 16 Apr 2020 04:18:45: Done! INFO @ Thu, 16 Apr 2020 04:18:46: 4000000 pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (721 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 04:18:53: 5000000 INFO @ Thu, 16 Apr 2020 04:19:00: 6000000 INFO @ Thu, 16 Apr 2020 04:19:04: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 04:19:04: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 04:19:04: #1 total tags in treatment: 3035259 INFO @ Thu, 16 Apr 2020 04:19:04: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 04:19:04: #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 04:19:04: #1 tags after filtering in treatment: 2922604 INFO @ Thu, 16 Apr 2020 04:19:04: #1 Redundant rate of treatment: 0.04 INFO @ Thu, 16 Apr 2020 04:19:04: #1 finished! INFO @ Thu, 16 Apr 2020 04:19:04: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 04:19:04: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 04:19:05: #2 number of paired peaks: 1097 INFO @ Thu, 16 Apr 2020 04:19:05: start model_add_line... INFO @ Thu, 16 Apr 2020 04:19:05: start X-correlation... INFO @ Thu, 16 Apr 2020 04:19:05: end of X-cor INFO @ Thu, 16 Apr 2020 04:19:05: #2 finished! INFO @ Thu, 16 Apr 2020 04:19:05: #2 predicted fragment length is 188 bps INFO @ Thu, 16 Apr 2020 04:19:05: #2 alternative fragment length(s) may be 188 bps INFO @ Thu, 16 Apr 2020 04:19:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.20_model.r WARNING @ Thu, 16 Apr 2020 04:19:05: #2 Since the d (188) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 04:19:05: #2 You may need to consider one of the other alternative d(s): 188 WARNING @ Thu, 16 Apr 2020 04:19:05: #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 04:19:05: #3 Call peaks... INFO @ Thu, 16 Apr 2020 04:19:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 04:19:11: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 04:19:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.20_peaks.xls INFO @ Thu, 16 Apr 2020 04:19:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 04:19:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6448059/SRX6448059.20_summits.bed INFO @ Thu, 16 Apr 2020 04:19:14: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (348 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。