Job ID = 14167239 SRX = SRX8688904 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 8388381 spots for SRR12174256/SRR12174256.sra Written 8388381 spots for SRR12174256/SRR12174256.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167788 ("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: 00:02:45 8388381 reads; of these: 8388381 (100.00%) were unpaired; of these: 399111 (4.76%) aligned 0 times 5851747 (69.76%) aligned exactly 1 time 2137523 (25.48%) aligned >1 times 95.24% overall alignment rate Time searching: 00:02:45 Overall time: 00:02:45 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] 314608 / 7989270 = 0.0394 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 @ Fri, 10 Dec 2021 11:17:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.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 @ Fri, 10 Dec 2021 11:17:16: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:17:16: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:17:23: 1000000 INFO @ Fri, 10 Dec 2021 11:17:29: 2000000 INFO @ Fri, 10 Dec 2021 11:17:36: 3000000 INFO @ Fri, 10 Dec 2021 11:17:42: 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 @ Fri, 10 Dec 2021 11:17:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.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 @ Fri, 10 Dec 2021 11:17:46: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:17:46: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:17:49: 5000000 INFO @ Fri, 10 Dec 2021 11:17:52: 1000000 INFO @ Fri, 10 Dec 2021 11:17:56: 6000000 INFO @ Fri, 10 Dec 2021 11:17:59: 2000000 INFO @ Fri, 10 Dec 2021 11:18:03: 7000000 INFO @ Fri, 10 Dec 2021 11:18:05: 3000000 INFO @ Fri, 10 Dec 2021 11:18:08: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:18:08: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:18:08: #1 total tags in treatment: 7674662 INFO @ Fri, 10 Dec 2021 11:18:08: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:18:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:18:08: #1 tags after filtering in treatment: 7674662 INFO @ Fri, 10 Dec 2021 11:18:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:18:08: #1 finished! INFO @ Fri, 10 Dec 2021 11:18:08: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:18:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:18:09: #2 number of paired peaks: 179 WARNING @ Fri, 10 Dec 2021 11:18:09: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Fri, 10 Dec 2021 11:18:09: start model_add_line... INFO @ Fri, 10 Dec 2021 11:18:09: start X-correlation... INFO @ Fri, 10 Dec 2021 11:18:09: end of X-cor INFO @ Fri, 10 Dec 2021 11:18:09: #2 finished! INFO @ Fri, 10 Dec 2021 11:18:09: #2 predicted fragment length is 54 bps INFO @ Fri, 10 Dec 2021 11:18:09: #2 alternative fragment length(s) may be 54 bps INFO @ Fri, 10 Dec 2021 11:18:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.05_model.r WARNING @ Fri, 10 Dec 2021 11:18:09: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:18:09: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Fri, 10 Dec 2021 11:18:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:18:09: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:18:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:18:12: 4000000 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 @ Fri, 10 Dec 2021 11:18:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.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 @ Fri, 10 Dec 2021 11:18:16: #1 read tag files... INFO @ Fri, 10 Dec 2021 11:18:16: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 11:18:18: 5000000 INFO @ Fri, 10 Dec 2021 11:18:22: 1000000 INFO @ Fri, 10 Dec 2021 11:18:23: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:18:24: 6000000 INFO @ Fri, 10 Dec 2021 11:18:28: 2000000 INFO @ Fri, 10 Dec 2021 11:18:30: 7000000 INFO @ Fri, 10 Dec 2021 11:18:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.05_peaks.xls INFO @ Fri, 10 Dec 2021 11:18:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:18:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.05_summits.bed INFO @ Fri, 10 Dec 2021 11:18:31: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1312 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:18:34: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:18:34: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:18:34: #1 total tags in treatment: 7674662 INFO @ Fri, 10 Dec 2021 11:18:34: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:18:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:18:35: 3000000 INFO @ Fri, 10 Dec 2021 11:18:35: #1 tags after filtering in treatment: 7674662 INFO @ Fri, 10 Dec 2021 11:18:35: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:18:35: #1 finished! INFO @ Fri, 10 Dec 2021 11:18:35: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:18:35: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:18:35: #2 number of paired peaks: 179 WARNING @ Fri, 10 Dec 2021 11:18:35: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Fri, 10 Dec 2021 11:18:35: start model_add_line... INFO @ Fri, 10 Dec 2021 11:18:35: start X-correlation... INFO @ Fri, 10 Dec 2021 11:18:35: end of X-cor INFO @ Fri, 10 Dec 2021 11:18:35: #2 finished! INFO @ Fri, 10 Dec 2021 11:18:35: #2 predicted fragment length is 54 bps INFO @ Fri, 10 Dec 2021 11:18:35: #2 alternative fragment length(s) may be 54 bps INFO @ Fri, 10 Dec 2021 11:18:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.10_model.r WARNING @ Fri, 10 Dec 2021 11:18:35: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:18:35: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Fri, 10 Dec 2021 11:18:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:18:35: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:18:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 11:18:40: 4000000 INFO @ Fri, 10 Dec 2021 11:18:46: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 11:18:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:18:52: 6000000 INFO @ Fri, 10 Dec 2021 11:18:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.10_peaks.xls INFO @ Fri, 10 Dec 2021 11:18:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:18:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.10_summits.bed INFO @ Fri, 10 Dec 2021 11:18:57: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (973 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 11:18:58: 7000000 INFO @ Fri, 10 Dec 2021 11:19:02: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 11:19:02: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 11:19:02: #1 total tags in treatment: 7674662 INFO @ Fri, 10 Dec 2021 11:19:02: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 11:19:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Dec 2021 11:19:03: #1 tags after filtering in treatment: 7674662 INFO @ Fri, 10 Dec 2021 11:19:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 11:19:03: #1 finished! INFO @ Fri, 10 Dec 2021 11:19:03: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 11:19:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 11:19:03: #2 number of paired peaks: 179 WARNING @ Fri, 10 Dec 2021 11:19:03: Fewer paired peaks (179) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 179 pairs to build model! INFO @ Fri, 10 Dec 2021 11:19:03: start model_add_line... INFO @ Fri, 10 Dec 2021 11:19:03: start X-correlation... INFO @ Fri, 10 Dec 2021 11:19:03: end of X-cor INFO @ Fri, 10 Dec 2021 11:19:03: #2 finished! INFO @ Fri, 10 Dec 2021 11:19:03: #2 predicted fragment length is 54 bps INFO @ Fri, 10 Dec 2021 11:19:03: #2 alternative fragment length(s) may be 54 bps INFO @ Fri, 10 Dec 2021 11:19:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.20_model.r WARNING @ Fri, 10 Dec 2021 11:19:03: #2 Since the d (54) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 11:19:03: #2 You may need to consider one of the other alternative d(s): 54 WARNING @ Fri, 10 Dec 2021 11:19:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Dec 2021 11:19:03: #3 Call peaks... INFO @ Fri, 10 Dec 2021 11:19:03: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 11:19:18: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 11:19:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.20_peaks.xls INFO @ Fri, 10 Dec 2021 11:19:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 11:19:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688904/SRX8688904.20_summits.bed INFO @ Fri, 10 Dec 2021 11:19:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (666 records, 4 fields): 1 millis CompletedMACS2peakCalling