Job ID = 6454233 SRX = SRX193312 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:55:19 prefetch.2.10.7: 1) Downloading 'SRR585045'... 2020-06-21T08:55:19 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:57:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:57:14 prefetch.2.10.7: 'SRR585045' is valid 2020-06-21T08:57:14 prefetch.2.10.7: 1) 'SRR585045' was downloaded successfully Read 13618335 spots for SRR585045/SRR585045.sra Written 13618335 spots for SRR585045/SRR585045.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: 00:03:38 13618335 reads; of these: 13618335 (100.00%) were unpaired; of these: 6182311 (45.40%) aligned 0 times 3233578 (23.74%) aligned exactly 1 time 4202446 (30.86%) aligned >1 times 54.60% overall alignment rate Time searching: 00:03:38 Overall time: 00:03:38 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] 3487557 / 7436024 = 0.4690 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 18:03:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.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 18:03:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:03:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:03:37: 1000000 INFO @ Sun, 21 Jun 2020 18:03:43: 2000000 INFO @ Sun, 21 Jun 2020 18:03:50: 3000000 INFO @ Sun, 21 Jun 2020 18:03:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:03:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:03:56: #1 total tags in treatment: 3948467 INFO @ Sun, 21 Jun 2020 18:03:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:03:56: #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 18:03:56: #1 tags after filtering in treatment: 3948307 INFO @ Sun, 21 Jun 2020 18:03:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:03:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:03:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:03:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:03:57: #2 number of paired peaks: 2195 INFO @ Sun, 21 Jun 2020 18:03:57: start model_add_line... INFO @ Sun, 21 Jun 2020 18:03:57: start X-correlation... INFO @ Sun, 21 Jun 2020 18:03:57: end of X-cor INFO @ Sun, 21 Jun 2020 18:03:57: #2 finished! INFO @ Sun, 21 Jun 2020 18:03:57: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 18:03:57: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sun, 21 Jun 2020 18:03:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.05_model.r WARNING @ Sun, 21 Jun 2020 18:03:57: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:03:57: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sun, 21 Jun 2020 18:03:57: #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 18:03:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:03:57: #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 18:04:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.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 18:04:01: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:04:01: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:04:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:04:07: 1000000 INFO @ Sun, 21 Jun 2020 18:04:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:04:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:04:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.05_summits.bed INFO @ Sun, 21 Jun 2020 18:04:09: Done! pass1 - making usageList (661 chroms): 1 millis pass2 - checking and writing primary data (2731 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:04:14: 2000000 INFO @ Sun, 21 Jun 2020 18:04:20: 3000000 INFO @ Sun, 21 Jun 2020 18:04:26: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:04:26: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:04:26: #1 total tags in treatment: 3948467 INFO @ Sun, 21 Jun 2020 18:04:26: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:04:26: #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 18:04:26: #1 tags after filtering in treatment: 3948307 INFO @ Sun, 21 Jun 2020 18:04:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:04:26: #1 finished! INFO @ Sun, 21 Jun 2020 18:04:26: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:04:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:04:27: #2 number of paired peaks: 2195 INFO @ Sun, 21 Jun 2020 18:04:27: start model_add_line... INFO @ Sun, 21 Jun 2020 18:04:27: start X-correlation... INFO @ Sun, 21 Jun 2020 18:04:27: end of X-cor INFO @ Sun, 21 Jun 2020 18:04:27: #2 finished! INFO @ Sun, 21 Jun 2020 18:04:27: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 18:04:27: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sun, 21 Jun 2020 18:04:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.10_model.r WARNING @ Sun, 21 Jun 2020 18:04:27: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:04:27: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sun, 21 Jun 2020 18:04:27: #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 18:04:27: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:04:27: #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 18:04:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.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 18:04:31: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:04:31: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:04:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:04:37: 1000000 INFO @ Sun, 21 Jun 2020 18:04:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:04:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:04:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.10_summits.bed INFO @ Sun, 21 Jun 2020 18:04:40: Done! pass1 - making usageList (533 chroms): 1 millis pass2 - checking and writing primary data (1847 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:04:43: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:04:49: 3000000 INFO @ Sun, 21 Jun 2020 18:04:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 18:04:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 18:04:56: #1 total tags in treatment: 3948467 INFO @ Sun, 21 Jun 2020 18:04:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:04:56: #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 18:04:56: #1 tags after filtering in treatment: 3948307 INFO @ Sun, 21 Jun 2020 18:04:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:04:56: #1 finished! INFO @ Sun, 21 Jun 2020 18:04:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:04:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:04:56: #2 number of paired peaks: 2195 INFO @ Sun, 21 Jun 2020 18:04:56: start model_add_line... INFO @ Sun, 21 Jun 2020 18:04:56: start X-correlation... INFO @ Sun, 21 Jun 2020 18:04:56: end of X-cor INFO @ Sun, 21 Jun 2020 18:04:56: #2 finished! INFO @ Sun, 21 Jun 2020 18:04:56: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 18:04:56: #2 alternative fragment length(s) may be 4,50 bps INFO @ Sun, 21 Jun 2020 18:04:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.20_model.r WARNING @ Sun, 21 Jun 2020 18:04:57: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:04:57: #2 You may need to consider one of the other alternative d(s): 4,50 WARNING @ Sun, 21 Jun 2020 18:04:57: #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 18:04:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:04:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:05:05: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:05:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:05:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:05:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX193312/SRX193312.20_summits.bed INFO @ Sun, 21 Jun 2020 18:05:09: Done! pass1 - making usageList (337 chroms): 1 millis pass2 - checking and writing primary data (657 records, 4 fields): 10 millis CompletedMACS2peakCalling