Job ID = 14168078 SRX = SRX8688974 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 14121359 spots for SRR12174343/SRR12174343.sra Written 14121359 spots for SRR12174343/SRR12174343.sra fastq に変換しました。 bowtie でマッピング中... Your job 14168832 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:53 14121359 reads; of these: 14121359 (100.00%) were unpaired; of these: 331092 (2.34%) aligned 0 times 9592171 (67.93%) aligned exactly 1 time 4198096 (29.73%) aligned >1 times 97.66% overall alignment rate Time searching: 00:05:54 Overall time: 00:05:54 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_sort_core] merging from 8 files... [bam_rmdupse_core] 1148870 / 13790267 = 0.0833 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 15:18:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.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 15:18:13: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:18:13: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:18:19: 1000000 INFO @ Fri, 10 Dec 2021 15:18:25: 2000000 INFO @ Fri, 10 Dec 2021 15:18:31: 3000000 INFO @ Fri, 10 Dec 2021 15:18:37: 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 15:18:42: 5000000 INFO @ Fri, 10 Dec 2021 15:18:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.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 15:18:42: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:18:42: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:18:48: 6000000 INFO @ Fri, 10 Dec 2021 15:18:49: 1000000 INFO @ Fri, 10 Dec 2021 15:18:54: 7000000 INFO @ Fri, 10 Dec 2021 15:18:55: 2000000 INFO @ Fri, 10 Dec 2021 15:19:00: 8000000 INFO @ Fri, 10 Dec 2021 15:19:01: 3000000 INFO @ Fri, 10 Dec 2021 15:19:06: 9000000 INFO @ Fri, 10 Dec 2021 15:19:08: 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 15:19:12: 10000000 INFO @ Fri, 10 Dec 2021 15:19:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.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 15:19:12: #1 read tag files... INFO @ Fri, 10 Dec 2021 15:19:12: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 15:19:14: 5000000 INFO @ Fri, 10 Dec 2021 15:19:18: 11000000 INFO @ Fri, 10 Dec 2021 15:19:19: 1000000 INFO @ Fri, 10 Dec 2021 15:19:20: 6000000 INFO @ Fri, 10 Dec 2021 15:19:24: 12000000 INFO @ Fri, 10 Dec 2021 15:19:25: 2000000 INFO @ Fri, 10 Dec 2021 15:19:26: 7000000 INFO @ Fri, 10 Dec 2021 15:19:29: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:19:29: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:19:29: #1 total tags in treatment: 12641397 INFO @ Fri, 10 Dec 2021 15:19:29: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:19:29: #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 15:19:29: #1 tags after filtering in treatment: 12641397 INFO @ Fri, 10 Dec 2021 15:19:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:19:29: #1 finished! INFO @ Fri, 10 Dec 2021 15:19:29: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:19:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:19:30: #2 number of paired peaks: 232 WARNING @ Fri, 10 Dec 2021 15:19:30: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Fri, 10 Dec 2021 15:19:30: start model_add_line... INFO @ Fri, 10 Dec 2021 15:19:30: start X-correlation... INFO @ Fri, 10 Dec 2021 15:19:30: end of X-cor INFO @ Fri, 10 Dec 2021 15:19:30: #2 finished! INFO @ Fri, 10 Dec 2021 15:19:30: #2 predicted fragment length is 47 bps INFO @ Fri, 10 Dec 2021 15:19:30: #2 alternative fragment length(s) may be 47 bps INFO @ Fri, 10 Dec 2021 15:19:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.05_model.r WARNING @ Fri, 10 Dec 2021 15:19:30: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:19:30: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Fri, 10 Dec 2021 15:19:30: #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 15:19:30: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:19:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:19:32: 3000000 INFO @ Fri, 10 Dec 2021 15:19:32: 8000000 INFO @ Fri, 10 Dec 2021 15:19:37: 4000000 INFO @ Fri, 10 Dec 2021 15:19:38: 9000000 INFO @ Fri, 10 Dec 2021 15:19:43: 5000000 INFO @ Fri, 10 Dec 2021 15:19:44: 10000000 INFO @ Fri, 10 Dec 2021 15:19:49: 6000000 INFO @ Fri, 10 Dec 2021 15:19:50: 11000000 INFO @ Fri, 10 Dec 2021 15:19:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:19:55: 7000000 INFO @ Fri, 10 Dec 2021 15:19:57: 12000000 INFO @ Fri, 10 Dec 2021 15:20:01: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:20:01: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:20:01: #1 total tags in treatment: 12641397 INFO @ Fri, 10 Dec 2021 15:20:01: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:20:01: #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 15:20:01: #1 tags after filtering in treatment: 12641397 INFO @ Fri, 10 Dec 2021 15:20:01: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:20:01: #1 finished! INFO @ Fri, 10 Dec 2021 15:20:01: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:20:01: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:20:01: 8000000 INFO @ Fri, 10 Dec 2021 15:20:02: #2 number of paired peaks: 232 WARNING @ Fri, 10 Dec 2021 15:20:02: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Fri, 10 Dec 2021 15:20:02: start model_add_line... INFO @ Fri, 10 Dec 2021 15:20:02: start X-correlation... INFO @ Fri, 10 Dec 2021 15:20:02: end of X-cor INFO @ Fri, 10 Dec 2021 15:20:02: #2 finished! INFO @ Fri, 10 Dec 2021 15:20:02: #2 predicted fragment length is 47 bps INFO @ Fri, 10 Dec 2021 15:20:02: #2 alternative fragment length(s) may be 47 bps INFO @ Fri, 10 Dec 2021 15:20:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.10_model.r WARNING @ Fri, 10 Dec 2021 15:20:02: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:20:02: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Fri, 10 Dec 2021 15:20:02: #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 15:20:02: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:20:02: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 15:20:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.05_peaks.xls INFO @ Fri, 10 Dec 2021 15:20:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:20:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.05_summits.bed INFO @ Fri, 10 Dec 2021 15:20:05: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1625 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:20:07: 9000000 INFO @ Fri, 10 Dec 2021 15:20:13: 10000000 INFO @ Fri, 10 Dec 2021 15:20:18: 11000000 INFO @ Fri, 10 Dec 2021 15:20:24: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:20:24: 12000000 INFO @ Fri, 10 Dec 2021 15:20:28: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 15:20:28: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 15:20:28: #1 total tags in treatment: 12641397 INFO @ Fri, 10 Dec 2021 15:20:28: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 15:20:28: #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 15:20:28: #1 tags after filtering in treatment: 12641397 INFO @ Fri, 10 Dec 2021 15:20:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 15:20:28: #1 finished! INFO @ Fri, 10 Dec 2021 15:20:28: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 15:20:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 15:20:29: #2 number of paired peaks: 232 WARNING @ Fri, 10 Dec 2021 15:20:29: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Fri, 10 Dec 2021 15:20:29: start model_add_line... INFO @ Fri, 10 Dec 2021 15:20:29: start X-correlation... INFO @ Fri, 10 Dec 2021 15:20:29: end of X-cor INFO @ Fri, 10 Dec 2021 15:20:29: #2 finished! INFO @ Fri, 10 Dec 2021 15:20:29: #2 predicted fragment length is 47 bps INFO @ Fri, 10 Dec 2021 15:20:29: #2 alternative fragment length(s) may be 47 bps INFO @ Fri, 10 Dec 2021 15:20:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.20_model.r WARNING @ Fri, 10 Dec 2021 15:20:29: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 15:20:29: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Fri, 10 Dec 2021 15:20:29: #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 15:20:29: #3 Call peaks... INFO @ Fri, 10 Dec 2021 15:20:29: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 15:20:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.10_peaks.xls INFO @ Fri, 10 Dec 2021 15:20:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:20:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.10_summits.bed INFO @ Fri, 10 Dec 2021 15:20:36: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1170 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 15:20:51: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 15:21:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.20_peaks.xls INFO @ Fri, 10 Dec 2021 15:21:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 15:21:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8688974/SRX8688974.20_summits.bed INFO @ Fri, 10 Dec 2021 15:21:04: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (891 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。