Job ID = 14170488 SRX = SRX8689049 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6115717 spots for SRR12174192/SRR12174192.sra Written 6115717 spots for SRR12174192/SRR12174192.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170888 ("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: 00:01:38 6115717 reads; of these: 6115717 (100.00%) were unpaired; of these: 545839 (8.93%) aligned 0 times 4786184 (78.26%) aligned exactly 1 time 783694 (12.81%) aligned >1 times 91.07% overall alignment rate Time searching: 00:01:38 Overall time: 00:01:38 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] 184872 / 5569878 = 0.0332 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 06:59:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.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 06:59:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:59:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:59:54: 1000000 INFO @ Sat, 11 Dec 2021 06:59:59: 2000000 INFO @ Sat, 11 Dec 2021 07:00:04: 3000000 INFO @ Sat, 11 Dec 2021 07:00:09: 4000000 INFO @ Sat, 11 Dec 2021 07:00:13: 5000000 INFO @ Sat, 11 Dec 2021 07:00:15: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:00:15: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:00:15: #1 total tags in treatment: 5385006 INFO @ Sat, 11 Dec 2021 07:00:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:00:15: #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 07:00:15: #1 tags after filtering in treatment: 5385006 INFO @ Sat, 11 Dec 2021 07:00:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:00:15: #1 finished! INFO @ Sat, 11 Dec 2021 07:00:15: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:00:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:00:16: #2 number of paired peaks: 137 WARNING @ Sat, 11 Dec 2021 07:00:16: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Sat, 11 Dec 2021 07:00:16: start model_add_line... INFO @ Sat, 11 Dec 2021 07:00:16: start X-correlation... INFO @ Sat, 11 Dec 2021 07:00:16: end of X-cor INFO @ Sat, 11 Dec 2021 07:00:16: #2 finished! INFO @ Sat, 11 Dec 2021 07:00:16: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 07:00:16: #2 alternative fragment length(s) may be 49,476 bps INFO @ Sat, 11 Dec 2021 07:00:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.05_model.r WARNING @ Sat, 11 Dec 2021 07:00:16: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:00:16: #2 You may need to consider one of the other alternative d(s): 49,476 WARNING @ Sat, 11 Dec 2021 07:00:16: #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 07:00:16: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:00:16: #3 Pre-compute pvalue-qvalue table... 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 07:00:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.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 07:00:19: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:00:19: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:00:24: 1000000 INFO @ Sat, 11 Dec 2021 07:00:27: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:00:29: 2000000 INFO @ Sat, 11 Dec 2021 07:00:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:00:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:00:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.05_summits.bed INFO @ Sat, 11 Dec 2021 07:00:33: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (969 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:00:34: 3000000 INFO @ Sat, 11 Dec 2021 07:00:39: 4000000 INFO @ Sat, 11 Dec 2021 07:00:44: 5000000 INFO @ Sat, 11 Dec 2021 07:00:46: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:00:46: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:00:46: #1 total tags in treatment: 5385006 INFO @ Sat, 11 Dec 2021 07:00:46: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:00:46: #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 07:00:46: #1 tags after filtering in treatment: 5385006 INFO @ Sat, 11 Dec 2021 07:00:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:00:46: #1 finished! INFO @ Sat, 11 Dec 2021 07:00:46: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:00:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:00:46: #2 number of paired peaks: 137 WARNING @ Sat, 11 Dec 2021 07:00:46: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Sat, 11 Dec 2021 07:00:46: start model_add_line... INFO @ Sat, 11 Dec 2021 07:00:46: start X-correlation... INFO @ Sat, 11 Dec 2021 07:00:46: end of X-cor INFO @ Sat, 11 Dec 2021 07:00:46: #2 finished! INFO @ Sat, 11 Dec 2021 07:00:46: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 07:00:46: #2 alternative fragment length(s) may be 49,476 bps INFO @ Sat, 11 Dec 2021 07:00:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.10_model.r WARNING @ Sat, 11 Dec 2021 07:00:46: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:00:46: #2 You may need to consider one of the other alternative d(s): 49,476 WARNING @ Sat, 11 Dec 2021 07:00:46: #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 07:00:46: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:00:46: #3 Pre-compute pvalue-qvalue table... 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 07:00:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.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 07:00:49: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:00:49: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:00:54: 1000000 INFO @ Sat, 11 Dec 2021 07:00:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:00:59: 2000000 INFO @ Sat, 11 Dec 2021 07:01:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:01:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:01:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.10_summits.bed INFO @ Sat, 11 Dec 2021 07:01:03: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (717 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:01:04: 3000000 INFO @ Sat, 11 Dec 2021 07:01:09: 4000000 INFO @ Sat, 11 Dec 2021 07:01:14: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:01:16: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:01:16: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:01:16: #1 total tags in treatment: 5385006 INFO @ Sat, 11 Dec 2021 07:01:16: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:01:16: #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 07:01:16: #1 tags after filtering in treatment: 5385006 INFO @ Sat, 11 Dec 2021 07:01:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:01:16: #1 finished! INFO @ Sat, 11 Dec 2021 07:01:16: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:01:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:01:16: #2 number of paired peaks: 137 WARNING @ Sat, 11 Dec 2021 07:01:16: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Sat, 11 Dec 2021 07:01:16: start model_add_line... INFO @ Sat, 11 Dec 2021 07:01:16: start X-correlation... INFO @ Sat, 11 Dec 2021 07:01:16: end of X-cor INFO @ Sat, 11 Dec 2021 07:01:16: #2 finished! INFO @ Sat, 11 Dec 2021 07:01:16: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 07:01:16: #2 alternative fragment length(s) may be 49,476 bps INFO @ Sat, 11 Dec 2021 07:01:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.20_model.r WARNING @ Sat, 11 Dec 2021 07:01:16: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:01:16: #2 You may need to consider one of the other alternative d(s): 49,476 WARNING @ Sat, 11 Dec 2021 07:01:16: #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 07:01:16: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:01:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:01:27: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:01:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:01:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:01:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689049/SRX8689049.20_summits.bed INFO @ Sat, 11 Dec 2021 07:01:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (346 records, 4 fields): 1 millis CompletedMACS2peakCalling