Job ID = 14170677 SRX = SRX10000639 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 9473735 spots for SRR13606571/SRR13606571.sra Written 9473735 spots for SRR13606571/SRR13606571.sra fastq に変換しました。 bowtie でマッピング中... Your job 14171098 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:00:59 9473735 reads; of these: 9473735 (100.00%) were unpaired; of these: 8946361 (94.43%) aligned 0 times 318602 (3.36%) aligned exactly 1 time 208772 (2.20%) aligned >1 times 5.57% overall alignment rate Time searching: 00:00:59 Overall time: 00:00:59 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_rmdupse_core] 110358 / 527374 = 0.2093 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 08:00:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.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 @ Sat, 11 Dec 2021 08:00:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:00:34: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:00:36: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 08:00:36: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 08:00:36: #1 total tags in treatment: 417016 INFO @ Sat, 11 Dec 2021 08:00:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:00:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:00:36: #1 tags after filtering in treatment: 417016 INFO @ Sat, 11 Dec 2021 08:00:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:00:36: #1 finished! INFO @ Sat, 11 Dec 2021 08:00:36: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:00:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:00:36: #2 number of paired peaks: 1477 INFO @ Sat, 11 Dec 2021 08:00:36: start model_add_line... INFO @ Sat, 11 Dec 2021 08:00:36: start X-correlation... INFO @ Sat, 11 Dec 2021 08:00:36: end of X-cor INFO @ Sat, 11 Dec 2021 08:00:36: #2 finished! INFO @ Sat, 11 Dec 2021 08:00:36: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 08:00:36: #2 alternative fragment length(s) may be 51,217,250,394,464,583 bps INFO @ Sat, 11 Dec 2021 08:00:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.05_model.r WARNING @ Sat, 11 Dec 2021 08:00:36: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:00:36: #2 You may need to consider one of the other alternative d(s): 51,217,250,394,464,583 WARNING @ Sat, 11 Dec 2021 08:00:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:00:36: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:00:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:00:37: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:00:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:00:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:00:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.05_summits.bed INFO @ Sat, 11 Dec 2021 08:00:38: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (441 records, 4 fields): 1 millis CompletedMACS2peakCalling WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 08:01:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.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 @ Sat, 11 Dec 2021 08:01:04: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:01:04: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:01:06: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 08:01:06: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 08:01:06: #1 total tags in treatment: 417016 INFO @ Sat, 11 Dec 2021 08:01:06: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:01:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:01:06: #1 tags after filtering in treatment: 417016 INFO @ Sat, 11 Dec 2021 08:01:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:01:06: #1 finished! INFO @ Sat, 11 Dec 2021 08:01:06: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:01:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:01:06: #2 number of paired peaks: 1477 INFO @ Sat, 11 Dec 2021 08:01:06: start model_add_line... INFO @ Sat, 11 Dec 2021 08:01:06: start X-correlation... INFO @ Sat, 11 Dec 2021 08:01:06: end of X-cor INFO @ Sat, 11 Dec 2021 08:01:06: #2 finished! INFO @ Sat, 11 Dec 2021 08:01:06: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 08:01:06: #2 alternative fragment length(s) may be 51,217,250,394,464,583 bps INFO @ Sat, 11 Dec 2021 08:01:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.10_model.r WARNING @ Sat, 11 Dec 2021 08:01:06: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:01:06: #2 You may need to consider one of the other alternative d(s): 51,217,250,394,464,583 WARNING @ Sat, 11 Dec 2021 08:01:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:01:06: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:01:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:01:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:01:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:01:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:01:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.10_summits.bed INFO @ Sat, 11 Dec 2021 08:01:08: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (256 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 11 Dec 2021 08:01:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.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 @ Sat, 11 Dec 2021 08:01:34: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:01:34: #1 read treatment tags... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:01:36: #1 tag size is determined as 51 bps INFO @ Sat, 11 Dec 2021 08:01:36: #1 tag size = 51 INFO @ Sat, 11 Dec 2021 08:01:36: #1 total tags in treatment: 417016 INFO @ Sat, 11 Dec 2021 08:01:36: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:01:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Dec 2021 08:01:37: #1 tags after filtering in treatment: 417016 INFO @ Sat, 11 Dec 2021 08:01:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:01:37: #1 finished! INFO @ Sat, 11 Dec 2021 08:01:37: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:01:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:01:37: #2 number of paired peaks: 1477 INFO @ Sat, 11 Dec 2021 08:01:37: start model_add_line... INFO @ Sat, 11 Dec 2021 08:01:37: start X-correlation... INFO @ Sat, 11 Dec 2021 08:01:37: end of X-cor INFO @ Sat, 11 Dec 2021 08:01:37: #2 finished! INFO @ Sat, 11 Dec 2021 08:01:37: #2 predicted fragment length is 51 bps INFO @ Sat, 11 Dec 2021 08:01:37: #2 alternative fragment length(s) may be 51,217,250,394,464,583 bps INFO @ Sat, 11 Dec 2021 08:01:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.20_model.r WARNING @ Sat, 11 Dec 2021 08:01:37: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:01:37: #2 You may need to consider one of the other alternative d(s): 51,217,250,394,464,583 WARNING @ Sat, 11 Dec 2021 08:01:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Dec 2021 08:01:37: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:01:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:01:38: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:01:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:01:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:01:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX10000639/SRX10000639.20_summits.bed INFO @ Sat, 11 Dec 2021 08:01:38: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (128 records, 4 fields): 2 millis CompletedMACS2peakCalling