Job ID = 14170484 SRX = SRX8689045 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6550515 spots for SRR12174245/SRR12174245.sra Written 6550515 spots for SRR12174245/SRR12174245.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170883 ("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: 00:02:29 6550515 reads; of these: 6550515 (100.00%) were unpaired; of these: 247160 (3.77%) aligned 0 times 4569096 (69.75%) aligned exactly 1 time 1734259 (26.48%) aligned >1 times 96.23% overall alignment rate Time searching: 00:02:29 Overall time: 00:02:29 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] 257294 / 6303355 = 0.0408 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 06:59:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.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 06:59:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:59:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:59:51: 1000000 INFO @ Sat, 11 Dec 2021 06:59:58: 2000000 INFO @ Sat, 11 Dec 2021 07:00:04: 3000000 INFO @ Sat, 11 Dec 2021 07:00:10: 4000000 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 07:00:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.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 07:00:15: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:00:15: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:00:17: 5000000 INFO @ Sat, 11 Dec 2021 07:00:22: 1000000 INFO @ Sat, 11 Dec 2021 07:00:24: 6000000 INFO @ Sat, 11 Dec 2021 07:00:24: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:00:24: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:00:24: #1 total tags in treatment: 6046061 INFO @ Sat, 11 Dec 2021 07:00:24: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:00:24: #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 07:00:25: #1 tags after filtering in treatment: 6046061 INFO @ Sat, 11 Dec 2021 07:00:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:00:25: #1 finished! INFO @ Sat, 11 Dec 2021 07:00:25: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:00:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:00:25: #2 number of paired peaks: 236 WARNING @ Sat, 11 Dec 2021 07:00:25: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Sat, 11 Dec 2021 07:00:25: start model_add_line... INFO @ Sat, 11 Dec 2021 07:00:25: start X-correlation... INFO @ Sat, 11 Dec 2021 07:00:25: end of X-cor INFO @ Sat, 11 Dec 2021 07:00:25: #2 finished! INFO @ Sat, 11 Dec 2021 07:00:25: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 07:00:25: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 11 Dec 2021 07:00:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.05_model.r WARNING @ Sat, 11 Dec 2021 07:00:25: #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 07:00:25: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 11 Dec 2021 07:00:25: #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 07:00:25: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:00:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:00:30: 2000000 INFO @ Sat, 11 Dec 2021 07:00:36: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:00:36: 3000000 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 07:00:43: 4000000 INFO @ Sat, 11 Dec 2021 07:00:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:00:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:00:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.05_summits.bed INFO @ Sat, 11 Dec 2021 07:00:44: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1167 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:00:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.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 07:00:45: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:00:45: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:00:49: 5000000 INFO @ Sat, 11 Dec 2021 07:00:52: 1000000 INFO @ Sat, 11 Dec 2021 07:00:56: 6000000 INFO @ Sat, 11 Dec 2021 07:00:56: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:00:56: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:00:56: #1 total tags in treatment: 6046061 INFO @ Sat, 11 Dec 2021 07:00:56: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:00:56: #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 07:00:56: #1 tags after filtering in treatment: 6046061 INFO @ Sat, 11 Dec 2021 07:00:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:00:56: #1 finished! INFO @ Sat, 11 Dec 2021 07:00:56: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:00:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:00:57: #2 number of paired peaks: 236 WARNING @ Sat, 11 Dec 2021 07:00:57: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Sat, 11 Dec 2021 07:00:57: start model_add_line... INFO @ Sat, 11 Dec 2021 07:00:57: start X-correlation... INFO @ Sat, 11 Dec 2021 07:00:57: end of X-cor INFO @ Sat, 11 Dec 2021 07:00:57: #2 finished! INFO @ Sat, 11 Dec 2021 07:00:57: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 07:00:57: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 11 Dec 2021 07:00:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.10_model.r WARNING @ Sat, 11 Dec 2021 07:00:57: #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 07:00:57: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 11 Dec 2021 07:00:57: #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 07:00:57: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:00:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:01:00: 2000000 INFO @ Sat, 11 Dec 2021 07:01:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:01:08: 3000000 INFO @ Sat, 11 Dec 2021 07:01:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:01:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:01:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.10_summits.bed INFO @ Sat, 11 Dec 2021 07:01:15: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (935 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:01:16: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:01:24: 5000000 INFO @ Sat, 11 Dec 2021 07:01:32: 6000000 INFO @ Sat, 11 Dec 2021 07:01:32: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:01:32: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:01:32: #1 total tags in treatment: 6046061 INFO @ Sat, 11 Dec 2021 07:01:32: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:01:32: #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 07:01:32: #1 tags after filtering in treatment: 6046061 INFO @ Sat, 11 Dec 2021 07:01:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:01:32: #1 finished! INFO @ Sat, 11 Dec 2021 07:01:32: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:01:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:01:33: #2 number of paired peaks: 236 WARNING @ Sat, 11 Dec 2021 07:01:33: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Sat, 11 Dec 2021 07:01:33: start model_add_line... INFO @ Sat, 11 Dec 2021 07:01:33: start X-correlation... INFO @ Sat, 11 Dec 2021 07:01:33: end of X-cor INFO @ Sat, 11 Dec 2021 07:01:33: #2 finished! INFO @ Sat, 11 Dec 2021 07:01:33: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 07:01:33: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 11 Dec 2021 07:01:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.20_model.r WARNING @ Sat, 11 Dec 2021 07:01:33: #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 07:01:33: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 11 Dec 2021 07:01:33: #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 07:01:33: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:01:33: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:01:44: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:01:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:01:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:01:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689045/SRX8689045.20_summits.bed INFO @ Sat, 11 Dec 2021 07:01:51: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (640 records, 4 fields): 2 millis CompletedMACS2peakCalling