Job ID = 6457238 SRX = SRX4579158 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:35:43 prefetch.2.10.7: 1) Downloading 'SRR7722301'... 2020-06-21T11:35:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:40:03 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:40:03 prefetch.2.10.7: 1) 'SRR7722301' was downloaded successfully Read 46870695 spots for SRR7722301/SRR7722301.sra Written 46870695 spots for SRR7722301/SRR7722301.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: 00:06:03 46870695 reads; of these: 46870695 (100.00%) were unpaired; of these: 42724897 (91.15%) aligned 0 times 2856462 (6.09%) aligned exactly 1 time 1289336 (2.75%) aligned >1 times 8.85% overall alignment rate Time searching: 00:06:03 Overall time: 00:06:04 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] 534140 / 4145798 = 0.1288 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 20:50:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.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 20:50:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:50:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:51:04: 1000000 INFO @ Sun, 21 Jun 2020 20:51:12: 2000000 INFO @ Sun, 21 Jun 2020 20:51:19: 3000000 INFO @ Sun, 21 Jun 2020 20:51:23: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:51:23: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:51:23: #1 total tags in treatment: 3611658 INFO @ Sun, 21 Jun 2020 20:51:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:51:23: #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 20:51:24: #1 tags after filtering in treatment: 3611473 INFO @ Sun, 21 Jun 2020 20:51:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:51:24: #1 finished! INFO @ Sun, 21 Jun 2020 20:51:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:51:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:51:24: #2 number of paired peaks: 1106 INFO @ Sun, 21 Jun 2020 20:51:24: start model_add_line... INFO @ Sun, 21 Jun 2020 20:51:24: start X-correlation... INFO @ Sun, 21 Jun 2020 20:51:24: end of X-cor INFO @ Sun, 21 Jun 2020 20:51:24: #2 finished! INFO @ Sun, 21 Jun 2020 20:51:24: #2 predicted fragment length is 66 bps INFO @ Sun, 21 Jun 2020 20:51:24: #2 alternative fragment length(s) may be 66,566,583 bps INFO @ Sun, 21 Jun 2020 20:51:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.05_model.r WARNING @ Sun, 21 Jun 2020 20:51:24: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:51:24: #2 You may need to consider one of the other alternative d(s): 66,566,583 WARNING @ Sun, 21 Jun 2020 20:51:24: #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 20:51:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:51:24: #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 @ Sun, 21 Jun 2020 20:51:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.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 20:51:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:51:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:51:32: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:51:34: 1000000 INFO @ Sun, 21 Jun 2020 20:51:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:51:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:51:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.05_summits.bed INFO @ Sun, 21 Jun 2020 20:51:37: Done! pass1 - making usageList (140 chroms): 1 millis pass2 - checking and writing primary data (647 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:51:41: 2000000 INFO @ Sun, 21 Jun 2020 20:51:48: 3000000 INFO @ Sun, 21 Jun 2020 20:51:53: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:51:53: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:51:53: #1 total tags in treatment: 3611658 INFO @ Sun, 21 Jun 2020 20:51:53: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:51:53: #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 20:51:53: #1 tags after filtering in treatment: 3611473 INFO @ Sun, 21 Jun 2020 20:51:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:51:53: #1 finished! INFO @ Sun, 21 Jun 2020 20:51:53: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:51:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:51:54: #2 number of paired peaks: 1106 INFO @ Sun, 21 Jun 2020 20:51:54: start model_add_line... INFO @ Sun, 21 Jun 2020 20:51:54: start X-correlation... INFO @ Sun, 21 Jun 2020 20:51:54: end of X-cor INFO @ Sun, 21 Jun 2020 20:51:54: #2 finished! INFO @ Sun, 21 Jun 2020 20:51:54: #2 predicted fragment length is 66 bps INFO @ Sun, 21 Jun 2020 20:51:54: #2 alternative fragment length(s) may be 66,566,583 bps INFO @ Sun, 21 Jun 2020 20:51:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.10_model.r WARNING @ Sun, 21 Jun 2020 20:51:54: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:51:54: #2 You may need to consider one of the other alternative d(s): 66,566,583 WARNING @ Sun, 21 Jun 2020 20:51:54: #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 20:51:54: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:51:54: #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 @ Sun, 21 Jun 2020 20:51:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.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 20:51:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:51:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:52:02: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:52:04: 1000000 INFO @ Sun, 21 Jun 2020 20:52:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:52:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:52:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.10_summits.bed INFO @ Sun, 21 Jun 2020 20:52:07: Done! pass1 - making usageList (77 chroms): 1 millis pass2 - checking and writing primary data (330 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:52:10: 2000000 INFO @ Sun, 21 Jun 2020 20:52:16: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:52:20: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:52:20: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:52:20: #1 total tags in treatment: 3611658 INFO @ Sun, 21 Jun 2020 20:52:20: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:52:20: #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 20:52:20: #1 tags after filtering in treatment: 3611473 INFO @ Sun, 21 Jun 2020 20:52:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:52:20: #1 finished! INFO @ Sun, 21 Jun 2020 20:52:20: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:52:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:52:20: #2 number of paired peaks: 1106 INFO @ Sun, 21 Jun 2020 20:52:20: start model_add_line... INFO @ Sun, 21 Jun 2020 20:52:20: start X-correlation... INFO @ Sun, 21 Jun 2020 20:52:21: end of X-cor INFO @ Sun, 21 Jun 2020 20:52:21: #2 finished! INFO @ Sun, 21 Jun 2020 20:52:21: #2 predicted fragment length is 66 bps INFO @ Sun, 21 Jun 2020 20:52:21: #2 alternative fragment length(s) may be 66,566,583 bps INFO @ Sun, 21 Jun 2020 20:52:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.20_model.r WARNING @ Sun, 21 Jun 2020 20:52:21: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:52:21: #2 You may need to consider one of the other alternative d(s): 66,566,583 WARNING @ Sun, 21 Jun 2020 20:52:21: #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 20:52:21: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:52:21: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:52:29: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:52:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:52:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:52:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4579158/SRX4579158.20_summits.bed INFO @ Sun, 21 Jun 2020 20:52:34: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (124 records, 4 fields): 2 millis CompletedMACS2peakCalling