Job ID = 5720558 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,210,489 reads read : 17,210,489 reads written : 17,210,489 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR5289702.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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:05 17210489 reads; of these: 17210489 (100.00%) were unpaired; of these: 1143211 (6.64%) aligned 0 times 11776263 (68.42%) aligned exactly 1 time 4291015 (24.93%) aligned >1 times 93.36% overall alignment rate Time searching: 00:08:05 Overall time: 00:08:05 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] 3482100 / 16067278 = 0.2167 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 00:44:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.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 00:44:02: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:44:02: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:44:09: 1000000 INFO @ Thu, 16 Apr 2020 00:44:16: 2000000 INFO @ Thu, 16 Apr 2020 00:44:23: 3000000 INFO @ Thu, 16 Apr 2020 00:44:29: 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 00:44:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.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 00:44:32: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:44:32: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:44:37: 5000000 INFO @ Thu, 16 Apr 2020 00:44:40: 1000000 INFO @ Thu, 16 Apr 2020 00:44:44: 6000000 INFO @ Thu, 16 Apr 2020 00:44:48: 2000000 INFO @ Thu, 16 Apr 2020 00:44:51: 7000000 INFO @ Thu, 16 Apr 2020 00:44:56: 3000000 INFO @ Thu, 16 Apr 2020 00:44:59: 8000000 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 00:45:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.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 00:45:02: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:45:02: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:45:04: 4000000 INFO @ Thu, 16 Apr 2020 00:45:06: 9000000 INFO @ Thu, 16 Apr 2020 00:45:10: 1000000 INFO @ Thu, 16 Apr 2020 00:45:11: 5000000 INFO @ Thu, 16 Apr 2020 00:45:14: 10000000 INFO @ Thu, 16 Apr 2020 00:45:18: 2000000 INFO @ Thu, 16 Apr 2020 00:45:19: 6000000 INFO @ Thu, 16 Apr 2020 00:45:22: 11000000 INFO @ Thu, 16 Apr 2020 00:45:25: 3000000 INFO @ Thu, 16 Apr 2020 00:45:27: 7000000 INFO @ Thu, 16 Apr 2020 00:45:29: 12000000 INFO @ Thu, 16 Apr 2020 00:45:33: 4000000 INFO @ Thu, 16 Apr 2020 00:45:33: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:45:33: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:45:33: #1 total tags in treatment: 12585178 INFO @ Thu, 16 Apr 2020 00:45:33: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:45:33: #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 00:45:34: #1 tags after filtering in treatment: 12585178 INFO @ Thu, 16 Apr 2020 00:45:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:45:34: #1 finished! INFO @ Thu, 16 Apr 2020 00:45:34: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:45:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:45:35: #2 number of paired peaks: 122 WARNING @ Thu, 16 Apr 2020 00:45:35: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Thu, 16 Apr 2020 00:45:35: start model_add_line... INFO @ Thu, 16 Apr 2020 00:45:35: start X-correlation... INFO @ Thu, 16 Apr 2020 00:45:35: end of X-cor INFO @ Thu, 16 Apr 2020 00:45:35: #2 finished! INFO @ Thu, 16 Apr 2020 00:45:35: #2 predicted fragment length is 61 bps INFO @ Thu, 16 Apr 2020 00:45:35: #2 alternative fragment length(s) may be 61 bps INFO @ Thu, 16 Apr 2020 00:45:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.05_model.r WARNING @ Thu, 16 Apr 2020 00:45:35: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:45:35: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Thu, 16 Apr 2020 00:45:35: #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 00:45:35: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:45:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:45:35: 8000000 INFO @ Thu, 16 Apr 2020 00:45:41: 5000000 INFO @ Thu, 16 Apr 2020 00:45:43: 9000000 INFO @ Thu, 16 Apr 2020 00:45:49: 6000000 INFO @ Thu, 16 Apr 2020 00:45:51: 10000000 INFO @ Thu, 16 Apr 2020 00:45:57: 7000000 INFO @ Thu, 16 Apr 2020 00:45:59: 11000000 INFO @ Thu, 16 Apr 2020 00:46:00: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:46:05: 8000000 INFO @ Thu, 16 Apr 2020 00:46:07: 12000000 INFO @ Thu, 16 Apr 2020 00:46:11: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:46:11: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:46:11: #1 total tags in treatment: 12585178 INFO @ Thu, 16 Apr 2020 00:46:11: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:46:11: #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 00:46:11: #1 tags after filtering in treatment: 12585178 INFO @ Thu, 16 Apr 2020 00:46:11: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:46:11: #1 finished! INFO @ Thu, 16 Apr 2020 00:46:11: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:46:11: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:46:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:46:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:46:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.05_summits.bed INFO @ Thu, 16 Apr 2020 00:46:12: Done! INFO @ Thu, 16 Apr 2020 00:46:12: 9000000 pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (12808 records, 4 fields): 12 millis INFO @ Thu, 16 Apr 2020 00:46:13: #2 number of paired peaks: 122 WARNING @ Thu, 16 Apr 2020 00:46:13: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Thu, 16 Apr 2020 00:46:13: start model_add_line... CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:46:13: start X-correlation... INFO @ Thu, 16 Apr 2020 00:46:13: end of X-cor INFO @ Thu, 16 Apr 2020 00:46:13: #2 finished! INFO @ Thu, 16 Apr 2020 00:46:13: #2 predicted fragment length is 61 bps INFO @ Thu, 16 Apr 2020 00:46:13: #2 alternative fragment length(s) may be 61 bps INFO @ Thu, 16 Apr 2020 00:46:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.10_model.r WARNING @ Thu, 16 Apr 2020 00:46:13: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:46:13: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Thu, 16 Apr 2020 00:46:13: #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 00:46:13: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:46:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:46:20: 10000000 INFO @ Thu, 16 Apr 2020 00:46:27: 11000000 INFO @ Thu, 16 Apr 2020 00:46:34: 12000000 INFO @ Thu, 16 Apr 2020 00:46:36: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:46:38: #1 tag size is determined as 50 bps INFO @ Thu, 16 Apr 2020 00:46:38: #1 tag size = 50 INFO @ Thu, 16 Apr 2020 00:46:38: #1 total tags in treatment: 12585178 INFO @ Thu, 16 Apr 2020 00:46:38: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:46:38: #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 00:46:38: #1 tags after filtering in treatment: 12585178 INFO @ Thu, 16 Apr 2020 00:46:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 16 Apr 2020 00:46:38: #1 finished! INFO @ Thu, 16 Apr 2020 00:46:38: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:46:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:46:39: #2 number of paired peaks: 122 WARNING @ Thu, 16 Apr 2020 00:46:39: Fewer paired peaks (122) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 122 pairs to build model! INFO @ Thu, 16 Apr 2020 00:46:39: start model_add_line... INFO @ Thu, 16 Apr 2020 00:46:39: start X-correlation... INFO @ Thu, 16 Apr 2020 00:46:39: end of X-cor INFO @ Thu, 16 Apr 2020 00:46:39: #2 finished! INFO @ Thu, 16 Apr 2020 00:46:39: #2 predicted fragment length is 61 bps INFO @ Thu, 16 Apr 2020 00:46:39: #2 alternative fragment length(s) may be 61 bps INFO @ Thu, 16 Apr 2020 00:46:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.20_model.r WARNING @ Thu, 16 Apr 2020 00:46:39: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:46:39: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Thu, 16 Apr 2020 00:46:39: #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 00:46:39: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:46:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:46:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:46:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:46:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.10_summits.bed INFO @ Thu, 16 Apr 2020 00:46:48: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (8112 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:47:03: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:47:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:47:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:47:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592425/SRX2592425.20_summits.bed INFO @ Thu, 16 Apr 2020 00:47:15: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (2201 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。