Job ID = 6498638 SRX = SRX647437 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:52:06 prefetch.2.10.7: 1) Downloading 'SRR1508420'... 2020-06-25T23:52:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:55:38 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:55:38 prefetch.2.10.7: 1) 'SRR1508420' was downloaded successfully Read 18034392 spots for SRR1508420/SRR1508420.sra Written 18034392 spots for SRR1508420/SRR1508420.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: 00:11:57 18034392 reads; of these: 18034392 (100.00%) were unpaired; of these: 5186494 (28.76%) aligned 0 times 8874710 (49.21%) aligned exactly 1 time 3973188 (22.03%) aligned >1 times 71.24% overall alignment rate Time searching: 00:11:57 Overall time: 00:11:57 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] 10220202 / 12847898 = 0.7955 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 09:12:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.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 09:12:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:12:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:12:44: 1000000 INFO @ Fri, 26 Jun 2020 09:12:52: 2000000 INFO @ Fri, 26 Jun 2020 09:12:57: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:12:57: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:12:57: #1 total tags in treatment: 2627696 INFO @ Fri, 26 Jun 2020 09:12:57: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:12:57: #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 09:12:57: #1 tags after filtering in treatment: 2627696 INFO @ Fri, 26 Jun 2020 09:12:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:12:57: #1 finished! INFO @ Fri, 26 Jun 2020 09:12:57: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:12:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:12:58: #2 number of paired peaks: 2718 INFO @ Fri, 26 Jun 2020 09:12:58: start model_add_line... INFO @ Fri, 26 Jun 2020 09:12:58: start X-correlation... INFO @ Fri, 26 Jun 2020 09:12:58: end of X-cor INFO @ Fri, 26 Jun 2020 09:12:58: #2 finished! INFO @ Fri, 26 Jun 2020 09:12:58: #2 predicted fragment length is 91 bps INFO @ Fri, 26 Jun 2020 09:12:58: #2 alternative fragment length(s) may be 91 bps INFO @ Fri, 26 Jun 2020 09:12:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.05_model.r WARNING @ Fri, 26 Jun 2020 09:12:58: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:12:58: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Fri, 26 Jun 2020 09:12:58: #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 09:12:58: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:12:58: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:13:04: #3 Call peaks for each chromosome... 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 09:13:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.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 09:13:06: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:13:06: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:13:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:13:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:13:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.05_summits.bed INFO @ Fri, 26 Jun 2020 09:13:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3640 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:13:13: 1000000 INFO @ Fri, 26 Jun 2020 09:13:19: 2000000 INFO @ Fri, 26 Jun 2020 09:13:23: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:13:23: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:13:23: #1 total tags in treatment: 2627696 INFO @ Fri, 26 Jun 2020 09:13:23: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:13:23: #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 09:13:23: #1 tags after filtering in treatment: 2627696 INFO @ Fri, 26 Jun 2020 09:13:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:13:23: #1 finished! INFO @ Fri, 26 Jun 2020 09:13:23: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:13:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:13:24: #2 number of paired peaks: 2718 INFO @ Fri, 26 Jun 2020 09:13:24: start model_add_line... INFO @ Fri, 26 Jun 2020 09:13:24: start X-correlation... INFO @ Fri, 26 Jun 2020 09:13:24: end of X-cor INFO @ Fri, 26 Jun 2020 09:13:24: #2 finished! INFO @ Fri, 26 Jun 2020 09:13:24: #2 predicted fragment length is 91 bps INFO @ Fri, 26 Jun 2020 09:13:24: #2 alternative fragment length(s) may be 91 bps INFO @ Fri, 26 Jun 2020 09:13:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.10_model.r WARNING @ Fri, 26 Jun 2020 09:13:24: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:13:24: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Fri, 26 Jun 2020 09:13:24: #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 09:13:24: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:13:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:13:30: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:13:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:13:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:13:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.10_summits.bed INFO @ Fri, 26 Jun 2020 09:13:33: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1421 records, 4 fields): 3 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 @ Fri, 26 Jun 2020 09:13:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.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 09:13:36: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:13:36: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:13:45: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:13:54: 2000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:14:00: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:14:00: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:14:00: #1 total tags in treatment: 2627696 INFO @ Fri, 26 Jun 2020 09:14:00: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:14:00: #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 09:14:00: #1 tags after filtering in treatment: 2627696 INFO @ Fri, 26 Jun 2020 09:14:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:14:00: #1 finished! INFO @ Fri, 26 Jun 2020 09:14:00: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:14:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:14:00: #2 number of paired peaks: 2718 INFO @ Fri, 26 Jun 2020 09:14:00: start model_add_line... INFO @ Fri, 26 Jun 2020 09:14:00: start X-correlation... INFO @ Fri, 26 Jun 2020 09:14:00: end of X-cor INFO @ Fri, 26 Jun 2020 09:14:00: #2 finished! INFO @ Fri, 26 Jun 2020 09:14:00: #2 predicted fragment length is 91 bps INFO @ Fri, 26 Jun 2020 09:14:00: #2 alternative fragment length(s) may be 91 bps INFO @ Fri, 26 Jun 2020 09:14:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.20_model.r WARNING @ Fri, 26 Jun 2020 09:14:00: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:14:00: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Fri, 26 Jun 2020 09:14:00: #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 09:14:00: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:14:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:14:07: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:14:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:14:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:14:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX647437/SRX647437.20_summits.bed INFO @ Fri, 26 Jun 2020 09:14:10: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (767 records, 4 fields): 2 millis CompletedMACS2peakCalling