Job ID = 12264870 SRX = SRX3032269 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 8260866 spots for SRR5863959/SRR5863959.sra Written 8260866 spots for SRR5863959/SRR5863959.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265047 ("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: 00:03:53 8260866 reads; of these: 8260866 (100.00%) were unpaired; of these: 2689402 (32.56%) aligned 0 times 4849269 (58.70%) aligned exactly 1 time 722195 (8.74%) aligned >1 times 67.44% overall alignment rate Time searching: 00:03:53 Overall time: 00:03:53 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] 1724143 / 5571464 = 0.3095 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:01:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.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, 03 Apr 2021 06:01:14: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:01:14: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:01:20: 1000000 INFO @ Sat, 03 Apr 2021 06:01:26: 2000000 INFO @ Sat, 03 Apr 2021 06:01:33: 3000000 INFO @ Sat, 03 Apr 2021 06:01:39: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:01:39: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:01:39: #1 total tags in treatment: 3847321 INFO @ Sat, 03 Apr 2021 06:01:39: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:01:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:01:39: #1 tags after filtering in treatment: 3847321 INFO @ Sat, 03 Apr 2021 06:01:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:01:39: #1 finished! INFO @ Sat, 03 Apr 2021 06:01:39: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:01:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:01:39: #2 number of paired peaks: 6154 INFO @ Sat, 03 Apr 2021 06:01:39: start model_add_line... INFO @ Sat, 03 Apr 2021 06:01:39: start X-correlation... INFO @ Sat, 03 Apr 2021 06:01:39: end of X-cor INFO @ Sat, 03 Apr 2021 06:01:39: #2 finished! INFO @ Sat, 03 Apr 2021 06:01:39: #2 predicted fragment length is 105 bps INFO @ Sat, 03 Apr 2021 06:01:39: #2 alternative fragment length(s) may be 105 bps INFO @ Sat, 03 Apr 2021 06:01:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.05_model.r WARNING @ Sat, 03 Apr 2021 06:01:39: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:01:39: #2 You may need to consider one of the other alternative d(s): 105 WARNING @ Sat, 03 Apr 2021 06:01:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:01:39: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:01:39: #3 Pre-compute pvalue-qvalue table... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:01:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.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, 03 Apr 2021 06:01:44: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:01:44: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:01:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:01:50: 1000000 INFO @ Sat, 03 Apr 2021 06:01:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:01:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:01:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.05_summits.bed INFO @ Sat, 03 Apr 2021 06:01:53: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (13150 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:01:56: 2000000 INFO @ Sat, 03 Apr 2021 06:02:02: 3000000 INFO @ Sat, 03 Apr 2021 06:02:07: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:02:07: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:02:07: #1 total tags in treatment: 3847321 INFO @ Sat, 03 Apr 2021 06:02:07: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:02:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:02:08: #1 tags after filtering in treatment: 3847321 INFO @ Sat, 03 Apr 2021 06:02:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:02:08: #1 finished! INFO @ Sat, 03 Apr 2021 06:02:08: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:02:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:02:08: #2 number of paired peaks: 6154 INFO @ Sat, 03 Apr 2021 06:02:08: start model_add_line... INFO @ Sat, 03 Apr 2021 06:02:08: start X-correlation... INFO @ Sat, 03 Apr 2021 06:02:08: end of X-cor INFO @ Sat, 03 Apr 2021 06:02:08: #2 finished! INFO @ Sat, 03 Apr 2021 06:02:08: #2 predicted fragment length is 105 bps INFO @ Sat, 03 Apr 2021 06:02:08: #2 alternative fragment length(s) may be 105 bps INFO @ Sat, 03 Apr 2021 06:02:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.10_model.r WARNING @ Sat, 03 Apr 2021 06:02:08: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:02:08: #2 You may need to consider one of the other alternative d(s): 105 WARNING @ Sat, 03 Apr 2021 06:02:08: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:02:08: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:02:08: #3 Pre-compute pvalue-qvalue table... BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:02:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.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, 03 Apr 2021 06:02:13: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:02:13: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:02:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:02:21: 1000000 INFO @ Sat, 03 Apr 2021 06:02:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:02:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:02:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.10_summits.bed INFO @ Sat, 03 Apr 2021 06:02:22: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8011 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:02:28: 2000000 INFO @ Sat, 03 Apr 2021 06:02:34: 3000000 INFO @ Sat, 03 Apr 2021 06:02:39: #1 tag size is determined as 74 bps INFO @ Sat, 03 Apr 2021 06:02:39: #1 tag size = 74 INFO @ Sat, 03 Apr 2021 06:02:39: #1 total tags in treatment: 3847321 INFO @ Sat, 03 Apr 2021 06:02:39: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:02:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:02:39: #1 tags after filtering in treatment: 3847321 INFO @ Sat, 03 Apr 2021 06:02:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Apr 2021 06:02:39: #1 finished! INFO @ Sat, 03 Apr 2021 06:02:39: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:02:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:02:39: #2 number of paired peaks: 6154 INFO @ Sat, 03 Apr 2021 06:02:39: start model_add_line... INFO @ Sat, 03 Apr 2021 06:02:39: start X-correlation... INFO @ Sat, 03 Apr 2021 06:02:39: end of X-cor INFO @ Sat, 03 Apr 2021 06:02:39: #2 finished! INFO @ Sat, 03 Apr 2021 06:02:39: #2 predicted fragment length is 105 bps INFO @ Sat, 03 Apr 2021 06:02:39: #2 alternative fragment length(s) may be 105 bps INFO @ Sat, 03 Apr 2021 06:02:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.20_model.r WARNING @ Sat, 03 Apr 2021 06:02:40: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:02:40: #2 You may need to consider one of the other alternative d(s): 105 WARNING @ Sat, 03 Apr 2021 06:02:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:02:40: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:02:40: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:02:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:02:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:02:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:02:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3032269/SRX3032269.20_summits.bed INFO @ Sat, 03 Apr 2021 06:02:53: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3239 records, 4 fields): 5 millis CompletedMACS2peakCalling BigWig に変換しました。