Job ID = 6458387 SRX = SRX511127 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:20:19 prefetch.2.10.7: 1) Downloading 'SRR1217232'... 2020-06-21T12:20:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:21:57 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:21:57 prefetch.2.10.7: 'SRR1217232' is valid 2020-06-21T12:21:57 prefetch.2.10.7: 1) 'SRR1217232' was downloaded successfully Read 9372883 spots for SRR1217232/SRR1217232.sra Written 9372883 spots for SRR1217232/SRR1217232.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: 00:04:04 9372883 reads; of these: 9372883 (100.00%) were unpaired; of these: 326902 (3.49%) aligned 0 times 2191851 (23.39%) aligned exactly 1 time 6854130 (73.13%) aligned >1 times 96.51% overall alignment rate Time searching: 00:04:05 Overall time: 00:04:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_rmdupse_core] 2587183 / 9045981 = 0.2860 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 @ Sun, 21 Jun 2020 21:29:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.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 @ Sun, 21 Jun 2020 21:29:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:29:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:29:06: 1000000 INFO @ Sun, 21 Jun 2020 21:29:12: 2000000 INFO @ Sun, 21 Jun 2020 21:29:18: 3000000 INFO @ Sun, 21 Jun 2020 21:29:23: 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 @ Sun, 21 Jun 2020 21:29:29: 5000000 INFO @ Sun, 21 Jun 2020 21:29:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.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 @ Sun, 21 Jun 2020 21:29:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:29:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:29:35: 6000000 INFO @ Sun, 21 Jun 2020 21:29:37: 1000000 INFO @ Sun, 21 Jun 2020 21:29:38: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:29:38: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:29:38: #1 total tags in treatment: 6458798 INFO @ Sun, 21 Jun 2020 21:29:38: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:29:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:29:39: #1 tags after filtering in treatment: 6458729 INFO @ Sun, 21 Jun 2020 21:29:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:29:39: #1 finished! INFO @ Sun, 21 Jun 2020 21:29:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:29:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:29:40: #2 number of paired peaks: 5161 INFO @ Sun, 21 Jun 2020 21:29:40: start model_add_line... INFO @ Sun, 21 Jun 2020 21:29:40: start X-correlation... INFO @ Sun, 21 Jun 2020 21:29:40: end of X-cor INFO @ Sun, 21 Jun 2020 21:29:40: #2 finished! INFO @ Sun, 21 Jun 2020 21:29:40: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 21:29:40: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 21 Jun 2020 21:29:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.05_model.r WARNING @ Sun, 21 Jun 2020 21:29:40: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:29:40: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 21 Jun 2020 21:29:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:29:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:29:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:29:43: 2000000 INFO @ Sun, 21 Jun 2020 21:29:49: 3000000 INFO @ Sun, 21 Jun 2020 21:29:52: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:29:55: 4000000 INFO @ Sun, 21 Jun 2020 21:29:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:29:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:29:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.05_summits.bed INFO @ Sun, 21 Jun 2020 21:29:58: Done! pass1 - making usageList (928 chroms): 2 millis pass2 - checking and writing primary data (3950 records, 4 fields): 27 millis CompletedMACS2peakCalling 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 @ Sun, 21 Jun 2020 21:30:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.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 @ Sun, 21 Jun 2020 21:30:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:30:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:30:02: 5000000 INFO @ Sun, 21 Jun 2020 21:30:09: 1000000 INFO @ Sun, 21 Jun 2020 21:30:09: 6000000 INFO @ Sun, 21 Jun 2020 21:30:12: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:30:12: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:30:12: #1 total tags in treatment: 6458798 INFO @ Sun, 21 Jun 2020 21:30:12: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:30:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:30:12: #1 tags after filtering in treatment: 6458729 INFO @ Sun, 21 Jun 2020 21:30:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:30:12: #1 finished! INFO @ Sun, 21 Jun 2020 21:30:12: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:30:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:30:13: #2 number of paired peaks: 5161 INFO @ Sun, 21 Jun 2020 21:30:13: start model_add_line... INFO @ Sun, 21 Jun 2020 21:30:13: start X-correlation... INFO @ Sun, 21 Jun 2020 21:30:13: end of X-cor INFO @ Sun, 21 Jun 2020 21:30:13: #2 finished! INFO @ Sun, 21 Jun 2020 21:30:13: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 21:30:13: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 21 Jun 2020 21:30:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.10_model.r WARNING @ Sun, 21 Jun 2020 21:30:13: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:30:13: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 21 Jun 2020 21:30:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:30:13: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:30:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:30:16: 2000000 INFO @ Sun, 21 Jun 2020 21:30:23: 3000000 INFO @ Sun, 21 Jun 2020 21:30:27: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:30:30: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:30:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:30:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:30:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.10_summits.bed INFO @ Sun, 21 Jun 2020 21:30:33: Done! pass1 - making usageList (750 chroms): 1 millis pass2 - checking and writing primary data (2693 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:30:38: 5000000 BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:30:45: 6000000 INFO @ Sun, 21 Jun 2020 21:30:48: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:30:48: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:30:48: #1 total tags in treatment: 6458798 INFO @ Sun, 21 Jun 2020 21:30:48: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:30:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:30:48: #1 tags after filtering in treatment: 6458729 INFO @ Sun, 21 Jun 2020 21:30:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:30:48: #1 finished! INFO @ Sun, 21 Jun 2020 21:30:48: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:30:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:30:49: #2 number of paired peaks: 5161 INFO @ Sun, 21 Jun 2020 21:30:49: start model_add_line... INFO @ Sun, 21 Jun 2020 21:30:49: start X-correlation... INFO @ Sun, 21 Jun 2020 21:30:49: end of X-cor INFO @ Sun, 21 Jun 2020 21:30:49: #2 finished! INFO @ Sun, 21 Jun 2020 21:30:49: #2 predicted fragment length is 53 bps INFO @ Sun, 21 Jun 2020 21:30:49: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 21 Jun 2020 21:30:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.20_model.r WARNING @ Sun, 21 Jun 2020 21:30:49: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:30:49: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 21 Jun 2020 21:30:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:30:49: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:30:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:31:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:31:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:31:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:31:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX511127/SRX511127.20_summits.bed INFO @ Sun, 21 Jun 2020 21:31:09: Done! pass1 - making usageList (600 chroms): 1 millis pass2 - checking and writing primary data (2025 records, 4 fields): 17 millis CompletedMACS2peakCalling