Job ID = 6458442 SRX = SRX5226996 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:30:22 prefetch.2.10.7: 1) Downloading 'SRR8417911'... 2020-06-21T12:30:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:31:36 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:31:37 prefetch.2.10.7: 'SRR8417911' is valid 2020-06-21T12:31:37 prefetch.2.10.7: 1) 'SRR8417911' was downloaded successfully 2020-06-21T12:31:37 prefetch.2.10.7: 'SRR8417911' has 0 unresolved dependencies Read 8155678 spots for SRR8417911/SRR8417911.sra Written 8155678 spots for SRR8417911/SRR8417911.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: 00:04:37 8155678 reads; of these: 8155678 (100.00%) were unpaired; of these: 2465191 (30.23%) aligned 0 times 1634358 (20.04%) aligned exactly 1 time 4056129 (49.73%) aligned >1 times 69.77% overall alignment rate Time searching: 00:04:37 Overall time: 00:04:37 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] 2239758 / 5690487 = 0.3936 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 21:38:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.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 21:38:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:38:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:38:55: 1000000 INFO @ Sun, 21 Jun 2020 21:39:01: 2000000 INFO @ Sun, 21 Jun 2020 21:39:07: 3000000 INFO @ Sun, 21 Jun 2020 21:39:09: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 21:39:09: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 21:39:09: #1 total tags in treatment: 3450729 INFO @ Sun, 21 Jun 2020 21:39:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:39:09: #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 21:39:10: #1 tags after filtering in treatment: 3450526 INFO @ Sun, 21 Jun 2020 21:39:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:39:10: #1 finished! INFO @ Sun, 21 Jun 2020 21:39:10: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:39:10: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:39:10: #2 number of paired peaks: 4539 INFO @ Sun, 21 Jun 2020 21:39:10: start model_add_line... INFO @ Sun, 21 Jun 2020 21:39:10: start X-correlation... INFO @ Sun, 21 Jun 2020 21:39:10: end of X-cor INFO @ Sun, 21 Jun 2020 21:39:10: #2 finished! INFO @ Sun, 21 Jun 2020 21:39:10: #2 predicted fragment length is 108 bps INFO @ Sun, 21 Jun 2020 21:39:10: #2 alternative fragment length(s) may be 108 bps INFO @ Sun, 21 Jun 2020 21:39:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.05_model.r WARNING @ Sun, 21 Jun 2020 21:39:10: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:39:10: #2 You may need to consider one of the other alternative d(s): 108 WARNING @ Sun, 21 Jun 2020 21:39:10: #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 21:39:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:39:10: #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 21:39:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:39:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.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 21:39:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:39:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:39:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:39:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:39:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.05_summits.bed INFO @ Sun, 21 Jun 2020 21:39:23: Done! pass1 - making usageList (795 chroms): 1 millis pass2 - checking and writing primary data (4101 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:39:25: 1000000 INFO @ Sun, 21 Jun 2020 21:39:30: 2000000 INFO @ Sun, 21 Jun 2020 21:39:36: 3000000 INFO @ Sun, 21 Jun 2020 21:39:39: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 21:39:39: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 21:39:39: #1 total tags in treatment: 3450729 INFO @ Sun, 21 Jun 2020 21:39:39: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:39:39: #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 21:39:39: #1 tags after filtering in treatment: 3450526 INFO @ Sun, 21 Jun 2020 21:39:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:39:39: #1 finished! INFO @ Sun, 21 Jun 2020 21:39:39: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:39:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:39:40: #2 number of paired peaks: 4539 INFO @ Sun, 21 Jun 2020 21:39:40: start model_add_line... INFO @ Sun, 21 Jun 2020 21:39:40: start X-correlation... INFO @ Sun, 21 Jun 2020 21:39:40: end of X-cor INFO @ Sun, 21 Jun 2020 21:39:40: #2 finished! INFO @ Sun, 21 Jun 2020 21:39:40: #2 predicted fragment length is 108 bps INFO @ Sun, 21 Jun 2020 21:39:40: #2 alternative fragment length(s) may be 108 bps INFO @ Sun, 21 Jun 2020 21:39:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.10_model.r WARNING @ Sun, 21 Jun 2020 21:39:40: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:39:40: #2 You may need to consider one of the other alternative d(s): 108 WARNING @ Sun, 21 Jun 2020 21:39:40: #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 21:39:40: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:39:40: #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 21:39:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:39:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.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 21:39:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:39:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:39:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:39:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:39:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.10_summits.bed INFO @ Sun, 21 Jun 2020 21:39:53: Done! pass1 - making usageList (701 chroms): 1 millis pass2 - checking and writing primary data (2731 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:39:55: 1000000 INFO @ Sun, 21 Jun 2020 21:40:00: 2000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:40:06: 3000000 INFO @ Sun, 21 Jun 2020 21:40:09: #1 tag size is determined as 74 bps INFO @ Sun, 21 Jun 2020 21:40:09: #1 tag size = 74 INFO @ Sun, 21 Jun 2020 21:40:09: #1 total tags in treatment: 3450729 INFO @ Sun, 21 Jun 2020 21:40:09: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:40:09: #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 21:40:09: #1 tags after filtering in treatment: 3450526 INFO @ Sun, 21 Jun 2020 21:40:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:40:09: #1 finished! INFO @ Sun, 21 Jun 2020 21:40:09: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:40:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:40:10: #2 number of paired peaks: 4539 INFO @ Sun, 21 Jun 2020 21:40:10: start model_add_line... INFO @ Sun, 21 Jun 2020 21:40:10: start X-correlation... INFO @ Sun, 21 Jun 2020 21:40:10: end of X-cor INFO @ Sun, 21 Jun 2020 21:40:10: #2 finished! INFO @ Sun, 21 Jun 2020 21:40:10: #2 predicted fragment length is 108 bps INFO @ Sun, 21 Jun 2020 21:40:10: #2 alternative fragment length(s) may be 108 bps INFO @ Sun, 21 Jun 2020 21:40:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.20_model.r WARNING @ Sun, 21 Jun 2020 21:40:10: #2 Since the d (108) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:40:10: #2 You may need to consider one of the other alternative d(s): 108 WARNING @ Sun, 21 Jun 2020 21:40:10: #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 21:40:10: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:40:10: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:40:19: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:40:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:40:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:40:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5226996/SRX5226996.20_summits.bed INFO @ Sun, 21 Jun 2020 21:40:23: Done! pass1 - making usageList (550 chroms): 1 millis pass2 - checking and writing primary data (1523 records, 4 fields): 15 millis CompletedMACS2peakCalling