Job ID = 6498644 SRX = SRX647442 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-26T00:11:35 prefetch.2.10.7: 1) Downloading 'SRR1508425'... 2020-06-26T00:11:35 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:14:50 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:14:50 prefetch.2.10.7: 1) 'SRR1508425' was downloaded successfully Read 19513100 spots for SRR1508425/SRR1508425.sra Written 19513100 spots for SRR1508425/SRR1508425.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: 00:13:13 19513100 reads; of these: 19513100 (100.00%) were unpaired; of these: 6079013 (31.15%) aligned 0 times 9682677 (49.62%) aligned exactly 1 time 3751410 (19.23%) aligned >1 times 68.85% overall alignment rate Time searching: 00:13:13 Overall time: 00:13:13 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] 10035754 / 13434087 = 0.7470 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 09:33:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.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 09:33:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:33:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:33:44: 1000000 INFO @ Fri, 26 Jun 2020 09:33:52: 2000000 INFO @ Fri, 26 Jun 2020 09:34:01: 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 @ Fri, 26 Jun 2020 09:34:04: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:34:04: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:34:04: #1 total tags in treatment: 3398333 INFO @ Fri, 26 Jun 2020 09:34:04: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:34:04: #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 09:34:04: #1 tags after filtering in treatment: 3398333 INFO @ Fri, 26 Jun 2020 09:34:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:34:04: #1 finished! INFO @ Fri, 26 Jun 2020 09:34:04: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:34:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:34:05: #2 number of paired peaks: 989 WARNING @ Fri, 26 Jun 2020 09:34:05: Fewer paired peaks (989) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 989 pairs to build model! INFO @ Fri, 26 Jun 2020 09:34:05: start model_add_line... INFO @ Fri, 26 Jun 2020 09:34:05: start X-correlation... INFO @ Fri, 26 Jun 2020 09:34:05: end of X-cor INFO @ Fri, 26 Jun 2020 09:34:05: #2 finished! INFO @ Fri, 26 Jun 2020 09:34:05: #2 predicted fragment length is 79 bps INFO @ Fri, 26 Jun 2020 09:34:05: #2 alternative fragment length(s) may be 79 bps INFO @ Fri, 26 Jun 2020 09:34:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.05_model.r WARNING @ Fri, 26 Jun 2020 09:34:05: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:34:05: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Fri, 26 Jun 2020 09:34:05: #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 09:34:05: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:34:05: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:34:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.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 09:34:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:34:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:34:14: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:34:17: 1000000 INFO @ Fri, 26 Jun 2020 09:34:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:34:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:34:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.05_summits.bed INFO @ Fri, 26 Jun 2020 09:34:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1955 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:34:27: 2000000 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 09:34:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.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 09:34:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:34:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:34:39: 3000000 INFO @ Fri, 26 Jun 2020 09:34:43: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:34:43: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:34:43: #1 total tags in treatment: 3398333 INFO @ Fri, 26 Jun 2020 09:34:43: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:34:43: #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 09:34:43: #1 tags after filtering in treatment: 3398333 INFO @ Fri, 26 Jun 2020 09:34:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:34:43: #1 finished! INFO @ Fri, 26 Jun 2020 09:34:43: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:34:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:34:44: #2 number of paired peaks: 989 WARNING @ Fri, 26 Jun 2020 09:34:44: Fewer paired peaks (989) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 989 pairs to build model! INFO @ Fri, 26 Jun 2020 09:34:44: start model_add_line... INFO @ Fri, 26 Jun 2020 09:34:44: start X-correlation... INFO @ Fri, 26 Jun 2020 09:34:44: end of X-cor INFO @ Fri, 26 Jun 2020 09:34:44: #2 finished! INFO @ Fri, 26 Jun 2020 09:34:44: #2 predicted fragment length is 79 bps INFO @ Fri, 26 Jun 2020 09:34:44: #2 alternative fragment length(s) may be 79 bps INFO @ Fri, 26 Jun 2020 09:34:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.10_model.r WARNING @ Fri, 26 Jun 2020 09:34:44: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:34:44: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Fri, 26 Jun 2020 09:34:44: #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 09:34:44: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:34:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:34:46: 1000000 INFO @ Fri, 26 Jun 2020 09:34:52: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:34:56: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:34:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:34:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:34:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.10_summits.bed INFO @ Fri, 26 Jun 2020 09:34:57: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1096 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:35:04: 3000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:35:08: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:35:08: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:35:08: #1 total tags in treatment: 3398333 INFO @ Fri, 26 Jun 2020 09:35:08: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:35:08: #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 09:35:08: #1 tags after filtering in treatment: 3398333 INFO @ Fri, 26 Jun 2020 09:35:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:35:08: #1 finished! INFO @ Fri, 26 Jun 2020 09:35:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:35:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:35:08: #2 number of paired peaks: 989 WARNING @ Fri, 26 Jun 2020 09:35:08: Fewer paired peaks (989) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 989 pairs to build model! INFO @ Fri, 26 Jun 2020 09:35:08: start model_add_line... INFO @ Fri, 26 Jun 2020 09:35:08: start X-correlation... INFO @ Fri, 26 Jun 2020 09:35:08: end of X-cor INFO @ Fri, 26 Jun 2020 09:35:08: #2 finished! INFO @ Fri, 26 Jun 2020 09:35:08: #2 predicted fragment length is 79 bps INFO @ Fri, 26 Jun 2020 09:35:08: #2 alternative fragment length(s) may be 79 bps INFO @ Fri, 26 Jun 2020 09:35:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.20_model.r WARNING @ Fri, 26 Jun 2020 09:35:08: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:35:08: #2 You may need to consider one of the other alternative d(s): 79 WARNING @ Fri, 26 Jun 2020 09:35:08: #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 09:35:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:35:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:35:17: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:35:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:35:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:35:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX647442/SRX647442.20_summits.bed INFO @ Fri, 26 Jun 2020 09:35:22: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (724 records, 4 fields): 3 millis CompletedMACS2peakCalling