Job ID = 14170560 SRX = SRX8689091 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 6859328 spots for SRR12174283/SRR12174283.sra Written 6859328 spots for SRR12174283/SRR12174283.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170966 ("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: 00:03:09 6859328 reads; of these: 6859328 (100.00%) were unpaired; of these: 222033 (3.24%) aligned 0 times 4368648 (63.69%) aligned exactly 1 time 2268647 (33.07%) aligned >1 times 96.76% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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] 304128 / 6637295 = 0.0458 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 07:20:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.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 07:20:10: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:20:10: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:20:15: 1000000 INFO @ Sat, 11 Dec 2021 07:20:20: 2000000 INFO @ Sat, 11 Dec 2021 07:20:26: 3000000 INFO @ Sat, 11 Dec 2021 07:20:31: 4000000 INFO @ Sat, 11 Dec 2021 07:20:37: 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 07:20:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.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 07:20:39: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:20:39: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:20:42: 6000000 INFO @ Sat, 11 Dec 2021 07:20:44: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:20:44: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:20:44: #1 total tags in treatment: 6333167 INFO @ Sat, 11 Dec 2021 07:20:44: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:20:44: #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 07:20:44: #1 tags after filtering in treatment: 6333167 INFO @ Sat, 11 Dec 2021 07:20:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:20:44: #1 finished! INFO @ Sat, 11 Dec 2021 07:20:44: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:20:44: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:20:45: #2 number of paired peaks: 413 WARNING @ Sat, 11 Dec 2021 07:20:45: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Sat, 11 Dec 2021 07:20:45: start model_add_line... INFO @ Sat, 11 Dec 2021 07:20:45: start X-correlation... INFO @ Sat, 11 Dec 2021 07:20:45: end of X-cor INFO @ Sat, 11 Dec 2021 07:20:45: #2 finished! INFO @ Sat, 11 Dec 2021 07:20:45: #2 predicted fragment length is 53 bps INFO @ Sat, 11 Dec 2021 07:20:45: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 11 Dec 2021 07:20:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.05_model.r WARNING @ Sat, 11 Dec 2021 07:20:45: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:20:45: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 11 Dec 2021 07:20:45: #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 07:20:45: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:20:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:20:45: 1000000 INFO @ Sat, 11 Dec 2021 07:20:51: 2000000 INFO @ Sat, 11 Dec 2021 07:20:57: 3000000 INFO @ Sat, 11 Dec 2021 07:20:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:21:02: 4000000 INFO @ Sat, 11 Dec 2021 07:21:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.05_peaks.xls INFO @ Sat, 11 Dec 2021 07:21:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:21:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.05_summits.bed INFO @ Sat, 11 Dec 2021 07:21:04: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1573 records, 4 fields): 3 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 07:21:08: 5000000 INFO @ Sat, 11 Dec 2021 07:21:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.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 07:21:09: #1 read tag files... INFO @ Sat, 11 Dec 2021 07:21:09: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 07:21:14: 6000000 INFO @ Sat, 11 Dec 2021 07:21:15: 1000000 INFO @ Sat, 11 Dec 2021 07:21:16: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:21:16: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:21:16: #1 total tags in treatment: 6333167 INFO @ Sat, 11 Dec 2021 07:21:16: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:21:16: #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 07:21:16: #1 tags after filtering in treatment: 6333167 INFO @ Sat, 11 Dec 2021 07:21:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:21:16: #1 finished! INFO @ Sat, 11 Dec 2021 07:21:16: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:21:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:21:16: #2 number of paired peaks: 413 WARNING @ Sat, 11 Dec 2021 07:21:16: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Sat, 11 Dec 2021 07:21:16: start model_add_line... INFO @ Sat, 11 Dec 2021 07:21:16: start X-correlation... INFO @ Sat, 11 Dec 2021 07:21:16: end of X-cor INFO @ Sat, 11 Dec 2021 07:21:16: #2 finished! INFO @ Sat, 11 Dec 2021 07:21:16: #2 predicted fragment length is 53 bps INFO @ Sat, 11 Dec 2021 07:21:16: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 11 Dec 2021 07:21:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.10_model.r WARNING @ Sat, 11 Dec 2021 07:21:16: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:21:16: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 11 Dec 2021 07:21:16: #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 07:21:16: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:21:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 07:21:21: 2000000 INFO @ Sat, 11 Dec 2021 07:21:27: 3000000 INFO @ Sat, 11 Dec 2021 07:21:30: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:21:33: 4000000 INFO @ Sat, 11 Dec 2021 07:21:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.10_peaks.xls INFO @ Sat, 11 Dec 2021 07:21:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:21:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.10_summits.bed INFO @ Sat, 11 Dec 2021 07:21:37: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1057 records, 4 fields): 67 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 07:21:39: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 07:21:44: 6000000 INFO @ Sat, 11 Dec 2021 07:21:46: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 07:21:46: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 07:21:46: #1 total tags in treatment: 6333167 INFO @ Sat, 11 Dec 2021 07:21:46: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 07:21:46: #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 07:21:46: #1 tags after filtering in treatment: 6333167 INFO @ Sat, 11 Dec 2021 07:21:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 07:21:46: #1 finished! INFO @ Sat, 11 Dec 2021 07:21:46: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 07:21:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 07:21:47: #2 number of paired peaks: 413 WARNING @ Sat, 11 Dec 2021 07:21:47: Fewer paired peaks (413) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 413 pairs to build model! INFO @ Sat, 11 Dec 2021 07:21:47: start model_add_line... INFO @ Sat, 11 Dec 2021 07:21:47: start X-correlation... INFO @ Sat, 11 Dec 2021 07:21:47: end of X-cor INFO @ Sat, 11 Dec 2021 07:21:47: #2 finished! INFO @ Sat, 11 Dec 2021 07:21:47: #2 predicted fragment length is 53 bps INFO @ Sat, 11 Dec 2021 07:21:47: #2 alternative fragment length(s) may be 53 bps INFO @ Sat, 11 Dec 2021 07:21:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.20_model.r WARNING @ Sat, 11 Dec 2021 07:21:47: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 07:21:47: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sat, 11 Dec 2021 07:21:47: #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 07:21:47: #3 Call peaks... INFO @ Sat, 11 Dec 2021 07:21:47: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 07:22:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 07:22:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.20_peaks.xls INFO @ Sat, 11 Dec 2021 07:22:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 07:22:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689091/SRX8689091.20_summits.bed INFO @ Sat, 11 Dec 2021 07:22:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (660 records, 4 fields): 359 millis CompletedMACS2peakCalling