Job ID = 6498613 SRX = SRX645122 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:42:57 prefetch.2.10.7: 1) Downloading 'SRR1505722'... 2020-06-25T23:42:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:57:21 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:57:21 prefetch.2.10.7: 1) 'SRR1505722' was downloaded successfully Read 53821965 spots for SRR1505722/SRR1505722.sra Written 53821965 spots for SRR1505722/SRR1505722.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: 00:18:27 53821965 reads; of these: 53821965 (100.00%) were unpaired; of these: 41223862 (76.59%) aligned 0 times 9741943 (18.10%) aligned exactly 1 time 2856160 (5.31%) aligned >1 times 23.41% overall alignment rate Time searching: 00:18:27 Overall time: 00:18:27 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] 9327305 / 12598103 = 0.7404 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 09:24:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.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 09:24:41: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:24:41: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:24:47: 1000000 INFO @ Fri, 26 Jun 2020 09:24:53: 2000000 INFO @ Fri, 26 Jun 2020 09:25:00: 3000000 INFO @ Fri, 26 Jun 2020 09:25:01: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:25:01: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:25:01: #1 total tags in treatment: 3270798 INFO @ Fri, 26 Jun 2020 09:25:01: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:25:01: #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 09:25:01: #1 tags after filtering in treatment: 3270798 INFO @ Fri, 26 Jun 2020 09:25:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:25:01: #1 finished! INFO @ Fri, 26 Jun 2020 09:25:01: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:25:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:25:02: #2 number of paired peaks: 2733 INFO @ Fri, 26 Jun 2020 09:25:02: start model_add_line... INFO @ Fri, 26 Jun 2020 09:25:02: start X-correlation... INFO @ Fri, 26 Jun 2020 09:25:02: end of X-cor INFO @ Fri, 26 Jun 2020 09:25:02: #2 finished! INFO @ Fri, 26 Jun 2020 09:25:02: #2 predicted fragment length is 129 bps INFO @ Fri, 26 Jun 2020 09:25:02: #2 alternative fragment length(s) may be 129 bps INFO @ Fri, 26 Jun 2020 09:25:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.05_model.r WARNING @ Fri, 26 Jun 2020 09:25:02: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:25:02: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Fri, 26 Jun 2020 09:25:02: #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 09:25:02: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:25:02: #3 Pre-compute pvalue-qvalue table... 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 09:25:09: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:25:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.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 09:25:10: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:25:10: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:25:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:25:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:25:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.05_summits.bed INFO @ Fri, 26 Jun 2020 09:25:13: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5520 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:25:17: 1000000 INFO @ Fri, 26 Jun 2020 09:25:24: 2000000 INFO @ Fri, 26 Jun 2020 09:25:32: 3000000 INFO @ Fri, 26 Jun 2020 09:25:34: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:25:34: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:25:34: #1 total tags in treatment: 3270798 INFO @ Fri, 26 Jun 2020 09:25:34: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:25:34: #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 09:25:34: #1 tags after filtering in treatment: 3270798 INFO @ Fri, 26 Jun 2020 09:25:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:25:34: #1 finished! INFO @ Fri, 26 Jun 2020 09:25:34: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:25:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:25:34: #2 number of paired peaks: 2733 INFO @ Fri, 26 Jun 2020 09:25:34: start model_add_line... INFO @ Fri, 26 Jun 2020 09:25:34: start X-correlation... INFO @ Fri, 26 Jun 2020 09:25:34: end of X-cor INFO @ Fri, 26 Jun 2020 09:25:34: #2 finished! INFO @ Fri, 26 Jun 2020 09:25:34: #2 predicted fragment length is 129 bps INFO @ Fri, 26 Jun 2020 09:25:34: #2 alternative fragment length(s) may be 129 bps INFO @ Fri, 26 Jun 2020 09:25:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.10_model.r WARNING @ Fri, 26 Jun 2020 09:25:34: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:25:34: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Fri, 26 Jun 2020 09:25:34: #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 09:25:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:25:34: #3 Pre-compute pvalue-qvalue table... 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 09:25:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.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 09:25:40: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:25:40: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:25:42: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:25:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:25:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:25:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.10_summits.bed INFO @ Fri, 26 Jun 2020 09:25:46: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3715 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:25:47: 1000000 INFO @ Fri, 26 Jun 2020 09:25:55: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:26:02: 3000000 INFO @ Fri, 26 Jun 2020 09:26:04: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:26:04: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:26:04: #1 total tags in treatment: 3270798 INFO @ Fri, 26 Jun 2020 09:26:04: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:26:04: #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 09:26:04: #1 tags after filtering in treatment: 3270798 INFO @ Fri, 26 Jun 2020 09:26:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:26:04: #1 finished! INFO @ Fri, 26 Jun 2020 09:26:04: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:26:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:26:05: #2 number of paired peaks: 2733 INFO @ Fri, 26 Jun 2020 09:26:05: start model_add_line... INFO @ Fri, 26 Jun 2020 09:26:05: start X-correlation... INFO @ Fri, 26 Jun 2020 09:26:05: end of X-cor INFO @ Fri, 26 Jun 2020 09:26:05: #2 finished! INFO @ Fri, 26 Jun 2020 09:26:05: #2 predicted fragment length is 129 bps INFO @ Fri, 26 Jun 2020 09:26:05: #2 alternative fragment length(s) may be 129 bps INFO @ Fri, 26 Jun 2020 09:26:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.20_model.r WARNING @ Fri, 26 Jun 2020 09:26:05: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:26:05: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Fri, 26 Jun 2020 09:26:05: #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 09:26:05: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:26:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:26:12: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:26:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:26:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:26:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645122/SRX645122.20_summits.bed INFO @ Fri, 26 Jun 2020 09:26:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2275 records, 4 fields): 4 millis CompletedMACS2peakCalling