Job ID = 6459063 SRX = SRX6386741 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T13:00:34 prefetch.2.10.7: 1) Downloading 'SRR9624473'... 2020-06-21T13:00:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T13:01:44 prefetch.2.10.7: HTTPS download succeed 2020-06-21T13:01:45 prefetch.2.10.7: 'SRR9624473' is valid 2020-06-21T13:01:45 prefetch.2.10.7: 1) 'SRR9624473' was downloaded successfully Read 5668271 spots for SRR9624473/SRR9624473.sra Written 5668271 spots for SRR9624473/SRR9624473.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: 00:01:10 5668271 reads; of these: 5668271 (100.00%) were unpaired; of these: 2550249 (44.99%) aligned 0 times 2249731 (39.69%) aligned exactly 1 time 868291 (15.32%) aligned >1 times 55.01% overall alignment rate Time searching: 00:01:10 Overall time: 00:01:10 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] 620471 / 3118022 = 0.1990 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 22:04:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.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 22:04:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:04:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:04:41: 1000000 INFO @ Sun, 21 Jun 2020 22:04:47: 2000000 INFO @ Sun, 21 Jun 2020 22:04:51: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:04:51: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:04:51: #1 total tags in treatment: 2497551 INFO @ Sun, 21 Jun 2020 22:04:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:04:51: #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 22:04:51: #1 tags after filtering in treatment: 2497527 INFO @ Sun, 21 Jun 2020 22:04:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:04:51: #1 finished! INFO @ Sun, 21 Jun 2020 22:04:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:04:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:04:51: #2 number of paired peaks: 727 WARNING @ Sun, 21 Jun 2020 22:04:51: Fewer paired peaks (727) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 727 pairs to build model! INFO @ Sun, 21 Jun 2020 22:04:51: start model_add_line... INFO @ Sun, 21 Jun 2020 22:04:51: start X-correlation... INFO @ Sun, 21 Jun 2020 22:04:51: end of X-cor INFO @ Sun, 21 Jun 2020 22:04:51: #2 finished! INFO @ Sun, 21 Jun 2020 22:04:51: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 22:04:51: #2 alternative fragment length(s) may be 54 bps INFO @ Sun, 21 Jun 2020 22:04:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.05_model.r WARNING @ Sun, 21 Jun 2020 22:04:51: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:04:51: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sun, 21 Jun 2020 22:04:51: #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 22:04:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:04:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:04:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:05:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:05:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:05:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.05_summits.bed INFO @ Sun, 21 Jun 2020 22:05:01: Done! pass1 - making usageList (363 chroms): 1 millis pass2 - checking and writing primary data (779 records, 4 fields): 12 millis CompletedMACS2peakCalling 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 22:05:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.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 22:05:04: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:05:04: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:05:11: 1000000 INFO @ Sun, 21 Jun 2020 22:05:19: 2000000 INFO @ Sun, 21 Jun 2020 22:05:23: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:05:23: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:05:23: #1 total tags in treatment: 2497551 INFO @ Sun, 21 Jun 2020 22:05:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:05:23: #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 22:05:24: #1 tags after filtering in treatment: 2497527 INFO @ Sun, 21 Jun 2020 22:05:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:05:24: #1 finished! INFO @ Sun, 21 Jun 2020 22:05:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:05:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:05:24: #2 number of paired peaks: 727 WARNING @ Sun, 21 Jun 2020 22:05:24: Fewer paired peaks (727) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 727 pairs to build model! INFO @ Sun, 21 Jun 2020 22:05:24: start model_add_line... INFO @ Sun, 21 Jun 2020 22:05:24: start X-correlation... INFO @ Sun, 21 Jun 2020 22:05:24: end of X-cor INFO @ Sun, 21 Jun 2020 22:05:24: #2 finished! INFO @ Sun, 21 Jun 2020 22:05:24: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 22:05:24: #2 alternative fragment length(s) may be 54 bps INFO @ Sun, 21 Jun 2020 22:05:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.10_model.r WARNING @ Sun, 21 Jun 2020 22:05:24: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:05:24: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sun, 21 Jun 2020 22:05:24: #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 22:05:24: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:05:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:05:30: #3 Call peaks for each chromosome... 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 22:05:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:05:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:05:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.10_summits.bed INFO @ Sun, 21 Jun 2020 22:05:33: Done! pass1 - making usageList (127 chroms): 1 millis pass2 - checking and writing primary data (281 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:05:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.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 22:05:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 22:05:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 22:05:40: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 22:05:47: 2000000 INFO @ Sun, 21 Jun 2020 22:05:51: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 22:05:51: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 22:05:51: #1 total tags in treatment: 2497551 INFO @ Sun, 21 Jun 2020 22:05:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:05:51: #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 22:05:51: #1 tags after filtering in treatment: 2497527 INFO @ Sun, 21 Jun 2020 22:05:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:05:51: #1 finished! INFO @ Sun, 21 Jun 2020 22:05:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:05:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:05:51: #2 number of paired peaks: 727 WARNING @ Sun, 21 Jun 2020 22:05:51: Fewer paired peaks (727) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 727 pairs to build model! INFO @ Sun, 21 Jun 2020 22:05:51: start model_add_line... INFO @ Sun, 21 Jun 2020 22:05:51: start X-correlation... INFO @ Sun, 21 Jun 2020 22:05:51: end of X-cor INFO @ Sun, 21 Jun 2020 22:05:51: #2 finished! INFO @ Sun, 21 Jun 2020 22:05:51: #2 predicted fragment length is 54 bps INFO @ Sun, 21 Jun 2020 22:05:51: #2 alternative fragment length(s) may be 54 bps INFO @ Sun, 21 Jun 2020 22:05:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.20_model.r WARNING @ Sun, 21 Jun 2020 22:05:51: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:05:51: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Sun, 21 Jun 2020 22:05:51: #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 22:05:51: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:05:51: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:05:58: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:06:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:06:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:06:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX6386741/SRX6386741.20_summits.bed INFO @ Sun, 21 Jun 2020 22:06:01: Done! pass1 - making usageList (81 chroms): 1 millis pass2 - checking and writing primary data (151 records, 4 fields): 4 millis CompletedMACS2peakCalling