Job ID = 6497915 SRX = SRX2592382 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T22:40:34 prefetch.2.10.7: 1) Downloading 'SRR5289659'... 2020-06-25T22:40:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T22:43:00 prefetch.2.10.7: HTTPS download succeed 2020-06-25T22:43:00 prefetch.2.10.7: 1) 'SRR5289659' was downloaded successfully Read 18118637 spots for SRR5289659/SRR5289659.sra Written 18118637 spots for SRR5289659/SRR5289659.sra 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: 00:08:00 18118637 reads; of these: 18118637 (100.00%) were unpaired; of these: 1141102 (6.30%) aligned 0 times 12243705 (67.58%) aligned exactly 1 time 4733830 (26.13%) aligned >1 times 93.70% overall alignment rate Time searching: 00:08:00 Overall time: 00:08:00 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] 4437029 / 16977535 = 0.2613 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 @ Fri, 26 Jun 2020 07:56:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.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 @ Fri, 26 Jun 2020 07:56:39: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:56:39: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:56:45: 1000000 INFO @ Fri, 26 Jun 2020 07:56:51: 2000000 INFO @ Fri, 26 Jun 2020 07:56:57: 3000000 INFO @ Fri, 26 Jun 2020 07:57:03: 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 @ Fri, 26 Jun 2020 07:57:09: 5000000 INFO @ Fri, 26 Jun 2020 07:57:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.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 @ Fri, 26 Jun 2020 07:57:09: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:57:09: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:57:15: 6000000 INFO @ Fri, 26 Jun 2020 07:57:15: 1000000 INFO @ Fri, 26 Jun 2020 07:57:21: 7000000 INFO @ Fri, 26 Jun 2020 07:57:22: 2000000 INFO @ Fri, 26 Jun 2020 07:57:27: 8000000 INFO @ Fri, 26 Jun 2020 07:57:28: 3000000 INFO @ Fri, 26 Jun 2020 07:57:33: 9000000 INFO @ Fri, 26 Jun 2020 07:57:34: 4000000 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 @ Fri, 26 Jun 2020 07:57:39: 10000000 INFO @ Fri, 26 Jun 2020 07:57:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.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 @ Fri, 26 Jun 2020 07:57:39: #1 read tag files... INFO @ Fri, 26 Jun 2020 07:57:39: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 07:57:40: 5000000 INFO @ Fri, 26 Jun 2020 07:57:46: 11000000 INFO @ Fri, 26 Jun 2020 07:57:46: 6000000 INFO @ Fri, 26 Jun 2020 07:57:46: 1000000 INFO @ Fri, 26 Jun 2020 07:57:52: 12000000 INFO @ Fri, 26 Jun 2020 07:57:53: 7000000 INFO @ Fri, 26 Jun 2020 07:57:54: 2000000 INFO @ Fri, 26 Jun 2020 07:57:56: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:57:56: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:57:56: #1 total tags in treatment: 12540506 INFO @ Fri, 26 Jun 2020 07:57:56: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:57:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:57:56: #1 tags after filtering in treatment: 12540506 INFO @ Fri, 26 Jun 2020 07:57:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:57:56: #1 finished! INFO @ Fri, 26 Jun 2020 07:57:56: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:57:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:57:57: #2 number of paired peaks: 212 WARNING @ Fri, 26 Jun 2020 07:57:57: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Fri, 26 Jun 2020 07:57:57: start model_add_line... INFO @ Fri, 26 Jun 2020 07:57:57: start X-correlation... INFO @ Fri, 26 Jun 2020 07:57:57: end of X-cor INFO @ Fri, 26 Jun 2020 07:57:57: #2 finished! INFO @ Fri, 26 Jun 2020 07:57:57: #2 predicted fragment length is 70 bps INFO @ Fri, 26 Jun 2020 07:57:57: #2 alternative fragment length(s) may be 70 bps INFO @ Fri, 26 Jun 2020 07:57:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.05_model.r WARNING @ Fri, 26 Jun 2020 07:57:57: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:57:57: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Fri, 26 Jun 2020 07:57:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:57:57: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:57:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:57:59: 8000000 INFO @ Fri, 26 Jun 2020 07:58:01: 3000000 INFO @ Fri, 26 Jun 2020 07:58:06: 9000000 INFO @ Fri, 26 Jun 2020 07:58:08: 4000000 INFO @ Fri, 26 Jun 2020 07:58:12: 10000000 INFO @ Fri, 26 Jun 2020 07:58:15: 5000000 INFO @ Fri, 26 Jun 2020 07:58:18: 11000000 INFO @ Fri, 26 Jun 2020 07:58:22: 6000000 INFO @ Fri, 26 Jun 2020 07:58:24: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:58:25: 12000000 INFO @ Fri, 26 Jun 2020 07:58:28: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:58:28: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:58:28: #1 total tags in treatment: 12540506 INFO @ Fri, 26 Jun 2020 07:58:28: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:58:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:58:28: #1 tags after filtering in treatment: 12540506 INFO @ Fri, 26 Jun 2020 07:58:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:58:28: #1 finished! INFO @ Fri, 26 Jun 2020 07:58:28: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:58:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:58:29: #2 number of paired peaks: 212 WARNING @ Fri, 26 Jun 2020 07:58:29: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Fri, 26 Jun 2020 07:58:29: start model_add_line... INFO @ Fri, 26 Jun 2020 07:58:29: 7000000 INFO @ Fri, 26 Jun 2020 07:58:29: start X-correlation... INFO @ Fri, 26 Jun 2020 07:58:29: end of X-cor INFO @ Fri, 26 Jun 2020 07:58:29: #2 finished! INFO @ Fri, 26 Jun 2020 07:58:29: #2 predicted fragment length is 70 bps INFO @ Fri, 26 Jun 2020 07:58:29: #2 alternative fragment length(s) may be 70 bps INFO @ Fri, 26 Jun 2020 07:58:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.10_model.r WARNING @ Fri, 26 Jun 2020 07:58:29: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:58:29: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Fri, 26 Jun 2020 07:58:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:58:29: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:58:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:58:36: 8000000 INFO @ Fri, 26 Jun 2020 07:58:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.05_peaks.xls INFO @ Fri, 26 Jun 2020 07:58:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:58:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.05_summits.bed INFO @ Fri, 26 Jun 2020 07:58:37: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5444 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 07:58:42: 9000000 INFO @ Fri, 26 Jun 2020 07:58:48: 10000000 INFO @ Fri, 26 Jun 2020 07:58:53: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:58:55: 11000000 INFO @ Fri, 26 Jun 2020 07:59:01: 12000000 INFO @ Fri, 26 Jun 2020 07:59:04: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 07:59:04: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 07:59:04: #1 total tags in treatment: 12540506 INFO @ Fri, 26 Jun 2020 07:59:04: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 07:59:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 07:59:05: #1 tags after filtering in treatment: 12540506 INFO @ Fri, 26 Jun 2020 07:59:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 07:59:05: #1 finished! INFO @ Fri, 26 Jun 2020 07:59:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 07:59:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 07:59:05: #2 number of paired peaks: 212 WARNING @ Fri, 26 Jun 2020 07:59:05: Fewer paired peaks (212) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 212 pairs to build model! INFO @ Fri, 26 Jun 2020 07:59:05: start model_add_line... INFO @ Fri, 26 Jun 2020 07:59:06: start X-correlation... INFO @ Fri, 26 Jun 2020 07:59:06: end of X-cor INFO @ Fri, 26 Jun 2020 07:59:06: #2 finished! INFO @ Fri, 26 Jun 2020 07:59:06: #2 predicted fragment length is 70 bps INFO @ Fri, 26 Jun 2020 07:59:06: #2 alternative fragment length(s) may be 70 bps INFO @ Fri, 26 Jun 2020 07:59:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.20_model.r WARNING @ Fri, 26 Jun 2020 07:59:06: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 07:59:06: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Fri, 26 Jun 2020 07:59:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 07:59:06: #3 Call peaks... INFO @ Fri, 26 Jun 2020 07:59:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 07:59:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.10_peaks.xls INFO @ Fri, 26 Jun 2020 07:59:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:59:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.10_summits.bed INFO @ Fri, 26 Jun 2020 07:59:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2386 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 07:59:30: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 07:59:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.20_peaks.xls INFO @ Fri, 26 Jun 2020 07:59:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 07:59:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2592382/SRX2592382.20_summits.bed INFO @ Fri, 26 Jun 2020 07:59:43: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (517 records, 4 fields): 2 millis CompletedMACS2peakCalling