Job ID = 14170433 SRX = SRX8689022 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6874631 spots for SRR12174327/SRR12174327.sra Written 6874631 spots for SRR12174327/SRR12174327.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170837 ("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: 00:02:04 6874631 reads; of these: 6874631 (100.00%) were unpaired; of these: 954266 (13.88%) aligned 0 times 4137725 (60.19%) aligned exactly 1 time 1782640 (25.93%) aligned >1 times 86.12% overall alignment rate Time searching: 00:02:04 Overall time: 00:02:04 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] 239115 / 5920365 = 0.0404 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 06:51:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.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 06:51:33: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:51:33: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:51:38: 1000000 INFO @ Sat, 11 Dec 2021 06:51:43: 2000000 INFO @ Sat, 11 Dec 2021 06:51:49: 3000000 INFO @ Sat, 11 Dec 2021 06:51:54: 4000000 INFO @ Sat, 11 Dec 2021 06:51:59: 5000000 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 06:52:02: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:52:02: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:52:02: #1 total tags in treatment: 5681250 INFO @ Sat, 11 Dec 2021 06:52:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:52:02: #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 06:52:02: #1 tags after filtering in treatment: 5681250 INFO @ Sat, 11 Dec 2021 06:52:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:52:02: #1 finished! INFO @ Sat, 11 Dec 2021 06:52:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:52:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:52:03: #2 number of paired peaks: 277 WARNING @ Sat, 11 Dec 2021 06:52:03: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sat, 11 Dec 2021 06:52:03: start model_add_line... INFO @ Sat, 11 Dec 2021 06:52:03: start X-correlation... INFO @ Sat, 11 Dec 2021 06:52:03: end of X-cor INFO @ Sat, 11 Dec 2021 06:52:03: #2 finished! INFO @ Sat, 11 Dec 2021 06:52:03: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 06:52:03: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 06:52:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.05_model.r WARNING @ Sat, 11 Dec 2021 06:52:03: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:52:03: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 06:52:03: #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 06:52:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:52:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:52:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.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 06:52:03: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:52:03: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:52:08: 1000000 INFO @ Sat, 11 Dec 2021 06:52:13: 2000000 INFO @ Sat, 11 Dec 2021 06:52:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:52:18: 3000000 INFO @ Sat, 11 Dec 2021 06:52:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:52:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:52:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.05_summits.bed INFO @ Sat, 11 Dec 2021 06:52:20: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (1350 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:52:23: 4000000 INFO @ Sat, 11 Dec 2021 06:52:28: 5000000 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 06:52:32: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:52:32: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:52:32: #1 total tags in treatment: 5681250 INFO @ Sat, 11 Dec 2021 06:52:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:52:32: #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 06:52:32: #1 tags after filtering in treatment: 5681250 INFO @ Sat, 11 Dec 2021 06:52:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:52:32: #1 finished! INFO @ Sat, 11 Dec 2021 06:52:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:52:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:52:32: #2 number of paired peaks: 277 WARNING @ Sat, 11 Dec 2021 06:52:32: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sat, 11 Dec 2021 06:52:32: start model_add_line... INFO @ Sat, 11 Dec 2021 06:52:32: start X-correlation... INFO @ Sat, 11 Dec 2021 06:52:32: end of X-cor INFO @ Sat, 11 Dec 2021 06:52:32: #2 finished! INFO @ Sat, 11 Dec 2021 06:52:32: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 06:52:32: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 06:52:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.10_model.r WARNING @ Sat, 11 Dec 2021 06:52:32: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:52:32: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 06:52:32: #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 06:52:32: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:52:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:52:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.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 06:52:33: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:52:33: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:52:38: 1000000 INFO @ Sat, 11 Dec 2021 06:52:43: 2000000 INFO @ Sat, 11 Dec 2021 06:52:44: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:52:48: 3000000 INFO @ Sat, 11 Dec 2021 06:52:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:52:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:52:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.10_summits.bed INFO @ Sat, 11 Dec 2021 06:52:49: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1106 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:52:53: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:52:58: 5000000 INFO @ Sat, 11 Dec 2021 06:53:02: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:53:02: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:53:02: #1 total tags in treatment: 5681250 INFO @ Sat, 11 Dec 2021 06:53:02: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:53:02: #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 06:53:02: #1 tags after filtering in treatment: 5681250 INFO @ Sat, 11 Dec 2021 06:53:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:53:02: #1 finished! INFO @ Sat, 11 Dec 2021 06:53:02: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:53:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:53:02: #2 number of paired peaks: 277 WARNING @ Sat, 11 Dec 2021 06:53:02: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sat, 11 Dec 2021 06:53:02: start model_add_line... INFO @ Sat, 11 Dec 2021 06:53:02: start X-correlation... INFO @ Sat, 11 Dec 2021 06:53:02: end of X-cor INFO @ Sat, 11 Dec 2021 06:53:02: #2 finished! INFO @ Sat, 11 Dec 2021 06:53:02: #2 predicted fragment length is 50 bps INFO @ Sat, 11 Dec 2021 06:53:02: #2 alternative fragment length(s) may be 50 bps INFO @ Sat, 11 Dec 2021 06:53:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.20_model.r WARNING @ Sat, 11 Dec 2021 06:53:02: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:53:02: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Sat, 11 Dec 2021 06:53:02: #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 06:53:02: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:53:02: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:53:14: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:53:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:53:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:53:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689022/SRX8689022.20_summits.bed INFO @ Sat, 11 Dec 2021 06:53:19: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (738 records, 4 fields): 2 millis CompletedMACS2peakCalling