Job ID = 5720663 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,714,179 reads read : 20,714,179 reads written : 20,714,179 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289759.sra.cache’: 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:34 20714179 reads; of these: 20714179 (100.00%) were unpaired; of these: 4387943 (21.18%) aligned 0 times 12461830 (60.16%) aligned exactly 1 time 3864406 (18.66%) aligned >1 times 78.82% overall alignment rate Time searching: 00:05:35 Overall time: 00:05:35 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_rmdupse_core] 2258706 / 16326236 = 0.1383 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 01:00:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.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 01:00:39: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:00:39: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:00:43: 1000000 INFO @ Thu, 16 Apr 2020 01:00:48: 2000000 INFO @ Thu, 16 Apr 2020 01:00:53: 3000000 INFO @ Thu, 16 Apr 2020 01:00:57: 4000000 INFO @ Thu, 16 Apr 2020 01:01:02: 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 @ Thu, 16 Apr 2020 01:01:07: 6000000 INFO @ Thu, 16 Apr 2020 01:01:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.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 01:01:08: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:01:08: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:01:12: 7000000 INFO @ Thu, 16 Apr 2020 01:01:12: 1000000 INFO @ Thu, 16 Apr 2020 01:01:17: 8000000 INFO @ Thu, 16 Apr 2020 01:01:17: 2000000 INFO @ Thu, 16 Apr 2020 01:01:21: 9000000 INFO @ Thu, 16 Apr 2020 01:01:22: 3000000 INFO @ Thu, 16 Apr 2020 01:01:26: 10000000 INFO @ Thu, 16 Apr 2020 01:01:27: 4000000 INFO @ Thu, 16 Apr 2020 01:01:31: 11000000 INFO @ Thu, 16 Apr 2020 01:01:32: 5000000 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 01:01:36: 12000000 INFO @ Thu, 16 Apr 2020 01:01:37: 6000000 INFO @ Thu, 16 Apr 2020 01:01:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.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 01:01:38: #1 read tag files... INFO @ Thu, 16 Apr 2020 01:01:38: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 01:01:41: 13000000 INFO @ Thu, 16 Apr 2020 01:01:41: 7000000 INFO @ Thu, 16 Apr 2020 01:01:43: 1000000 INFO @ Thu, 16 Apr 2020 01:01:46: 14000000 INFO @ Thu, 16 Apr 2020 01:01:46: 8000000 INFO @ Thu, 16 Apr 2020 01:01:46: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 01:01:46: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 01:01:46: #1 total tags in treatment: 14067530 INFO @ Thu, 16 Apr 2020 01:01:46: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:01:46: #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 01:01:47: #1 tags after filtering in treatment: 14067530 INFO @ Thu, 16 Apr 2020 01:01:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:01:47: #1 finished! INFO @ Thu, 16 Apr 2020 01:01:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:01:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:01:48: #2 number of paired peaks: 175 WARNING @ Thu, 16 Apr 2020 01:01:48: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Thu, 16 Apr 2020 01:01:48: start model_add_line... INFO @ Thu, 16 Apr 2020 01:01:48: start X-correlation... INFO @ Thu, 16 Apr 2020 01:01:48: end of X-cor INFO @ Thu, 16 Apr 2020 01:01:48: #2 finished! INFO @ Thu, 16 Apr 2020 01:01:48: #2 predicted fragment length is 50 bps INFO @ Thu, 16 Apr 2020 01:01:48: #2 alternative fragment length(s) may be 50 bps INFO @ Thu, 16 Apr 2020 01:01:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.05_model.r WARNING @ Thu, 16 Apr 2020 01:01:48: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:01:48: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Thu, 16 Apr 2020 01:01:48: #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 01:01:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:01:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:01:48: 2000000 INFO @ Thu, 16 Apr 2020 01:01:51: 9000000 INFO @ Thu, 16 Apr 2020 01:01:53: 3000000 INFO @ Thu, 16 Apr 2020 01:01:56: 10000000 INFO @ Thu, 16 Apr 2020 01:01:58: 4000000 INFO @ Thu, 16 Apr 2020 01:02:01: 11000000 INFO @ Thu, 16 Apr 2020 01:02:03: 5000000 INFO @ Thu, 16 Apr 2020 01:02:06: 12000000 INFO @ Thu, 16 Apr 2020 01:02:08: 6000000 INFO @ Thu, 16 Apr 2020 01:02:11: 13000000 INFO @ Thu, 16 Apr 2020 01:02:13: 7000000 INFO @ Thu, 16 Apr 2020 01:02:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:02:16: 14000000 INFO @ Thu, 16 Apr 2020 01:02:16: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 01:02:16: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 01:02:16: #1 total tags in treatment: 14067530 INFO @ Thu, 16 Apr 2020 01:02:16: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:02:16: #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 01:02:17: #1 tags after filtering in treatment: 14067530 INFO @ Thu, 16 Apr 2020 01:02:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:02:17: #1 finished! INFO @ Thu, 16 Apr 2020 01:02:17: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:02:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:02:17: 8000000 INFO @ Thu, 16 Apr 2020 01:02:17: #2 number of paired peaks: 175 WARNING @ Thu, 16 Apr 2020 01:02:17: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Thu, 16 Apr 2020 01:02:17: start model_add_line... INFO @ Thu, 16 Apr 2020 01:02:18: start X-correlation... INFO @ Thu, 16 Apr 2020 01:02:18: end of X-cor INFO @ Thu, 16 Apr 2020 01:02:18: #2 finished! INFO @ Thu, 16 Apr 2020 01:02:18: #2 predicted fragment length is 50 bps INFO @ Thu, 16 Apr 2020 01:02:18: #2 alternative fragment length(s) may be 50 bps INFO @ Thu, 16 Apr 2020 01:02:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.10_model.r WARNING @ Thu, 16 Apr 2020 01:02:18: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:02:18: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Thu, 16 Apr 2020 01:02:18: #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 01:02:18: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:02:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:02:22: 9000000 INFO @ Thu, 16 Apr 2020 01:02:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.05_peaks.xls INFO @ Thu, 16 Apr 2020 01:02:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:02:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.05_summits.bed INFO @ Thu, 16 Apr 2020 01:02:27: Done! INFO @ Thu, 16 Apr 2020 01:02:27: 10000000 pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2295 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:02:32: 11000000 INFO @ Thu, 16 Apr 2020 01:02:37: 12000000 INFO @ Thu, 16 Apr 2020 01:02:41: 13000000 INFO @ Thu, 16 Apr 2020 01:02:44: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:02:46: 14000000 INFO @ Thu, 16 Apr 2020 01:02:47: #1 tag size is determined as 51 bps INFO @ Thu, 16 Apr 2020 01:02:47: #1 tag size = 51 INFO @ Thu, 16 Apr 2020 01:02:47: #1 total tags in treatment: 14067530 INFO @ Thu, 16 Apr 2020 01:02:47: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 01:02:47: #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 01:02:47: #1 tags after filtering in treatment: 14067530 INFO @ Thu, 16 Apr 2020 01:02:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 01:02:47: #1 finished! INFO @ Thu, 16 Apr 2020 01:02:47: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 01:02:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 01:02:48: #2 number of paired peaks: 175 WARNING @ Thu, 16 Apr 2020 01:02:48: Fewer paired peaks (175) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 175 pairs to build model! INFO @ Thu, 16 Apr 2020 01:02:48: start model_add_line... INFO @ Thu, 16 Apr 2020 01:02:48: start X-correlation... INFO @ Thu, 16 Apr 2020 01:02:48: end of X-cor INFO @ Thu, 16 Apr 2020 01:02:48: #2 finished! INFO @ Thu, 16 Apr 2020 01:02:48: #2 predicted fragment length is 50 bps INFO @ Thu, 16 Apr 2020 01:02:48: #2 alternative fragment length(s) may be 50 bps INFO @ Thu, 16 Apr 2020 01:02:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.20_model.r WARNING @ Thu, 16 Apr 2020 01:02:48: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 01:02:48: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Thu, 16 Apr 2020 01:02:48: #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 01:02:48: #3 Call peaks... INFO @ Thu, 16 Apr 2020 01:02:48: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 01:02:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.10_peaks.xls INFO @ Thu, 16 Apr 2020 01:02:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:02:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.10_summits.bed INFO @ Thu, 16 Apr 2020 01:02:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1152 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 01:03:14: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 01:03:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.20_peaks.xls INFO @ Thu, 16 Apr 2020 01:03:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 01:03:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592482/SRX2592482.20_summits.bed INFO @ Thu, 16 Apr 2020 01:03:27: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (756 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。