Job ID = 14170390 SRX = SRX8689011 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 7199040 spots for SRR12174300/SRR12174300.sra Written 7199040 spots for SRR12174300/SRR12174300.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170791 ("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: 00:03:16 7199040 reads; of these: 7199040 (100.00%) were unpaired; of these: 264355 (3.67%) aligned 0 times 4922530 (68.38%) aligned exactly 1 time 2012155 (27.95%) aligned >1 times 96.33% overall alignment rate Time searching: 00:03:16 Overall time: 00:03:16 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] 1363722 / 6934685 = 0.1967 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 06:41:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.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 06:41:40: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:41:40: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:41:46: 1000000 INFO @ Sat, 11 Dec 2021 06:41:51: 2000000 INFO @ Sat, 11 Dec 2021 06:41:57: 3000000 INFO @ Sat, 11 Dec 2021 06:42:02: 4000000 INFO @ Sat, 11 Dec 2021 06:42:08: 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 06:42:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.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 06:42:10: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:42:10: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:42:11: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:42:11: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:42:11: #1 total tags in treatment: 5570963 INFO @ Sat, 11 Dec 2021 06:42:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:42:11: #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 06:42:11: #1 tags after filtering in treatment: 5570963 INFO @ Sat, 11 Dec 2021 06:42:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:42:11: #1 finished! INFO @ Sat, 11 Dec 2021 06:42:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:42:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:42:12: #2 number of paired peaks: 374 WARNING @ Sat, 11 Dec 2021 06:42:12: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Sat, 11 Dec 2021 06:42:12: start model_add_line... INFO @ Sat, 11 Dec 2021 06:42:12: start X-correlation... INFO @ Sat, 11 Dec 2021 06:42:12: end of X-cor INFO @ Sat, 11 Dec 2021 06:42:12: #2 finished! INFO @ Sat, 11 Dec 2021 06:42:12: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 06:42:12: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 11 Dec 2021 06:42:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.05_model.r WARNING @ Sat, 11 Dec 2021 06:42:12: #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 06:42:12: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 11 Dec 2021 06:42:12: #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 06:42:12: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:42:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:42:15: 1000000 INFO @ Sat, 11 Dec 2021 06:42:21: 2000000 INFO @ Sat, 11 Dec 2021 06:42:24: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:42:26: 3000000 INFO @ Sat, 11 Dec 2021 06:42:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:42:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:42:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.05_summits.bed INFO @ Sat, 11 Dec 2021 06:42:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1346 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:42:32: 4000000 INFO @ Sat, 11 Dec 2021 06:42:37: 5000000 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 06:42:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.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 06:42:40: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:42:40: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:42:41: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:42:41: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:42:41: #1 total tags in treatment: 5570963 INFO @ Sat, 11 Dec 2021 06:42:41: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:42:41: #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 06:42:41: #1 tags after filtering in treatment: 5570963 INFO @ Sat, 11 Dec 2021 06:42:41: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:42:41: #1 finished! INFO @ Sat, 11 Dec 2021 06:42:41: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:42:41: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:42:41: #2 number of paired peaks: 374 WARNING @ Sat, 11 Dec 2021 06:42:41: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Sat, 11 Dec 2021 06:42:41: start model_add_line... INFO @ Sat, 11 Dec 2021 06:42:41: start X-correlation... INFO @ Sat, 11 Dec 2021 06:42:41: end of X-cor INFO @ Sat, 11 Dec 2021 06:42:41: #2 finished! INFO @ Sat, 11 Dec 2021 06:42:41: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 06:42:41: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 11 Dec 2021 06:42:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.10_model.r WARNING @ Sat, 11 Dec 2021 06:42:41: #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 06:42:41: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 11 Dec 2021 06:42:41: #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 06:42:41: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:42:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:42:45: 1000000 INFO @ Sat, 11 Dec 2021 06:42:51: 2000000 INFO @ Sat, 11 Dec 2021 06:42:54: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:42:56: 3000000 INFO @ Sat, 11 Dec 2021 06:43:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:43:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:43:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.10_summits.bed INFO @ Sat, 11 Dec 2021 06:43:01: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1118 records, 4 fields): 52 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:43:02: 4000000 INFO @ Sat, 11 Dec 2021 06:43:07: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:43:10: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:43:10: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:43:10: #1 total tags in treatment: 5570963 INFO @ Sat, 11 Dec 2021 06:43:10: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:43:10: #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 06:43:10: #1 tags after filtering in treatment: 5570963 INFO @ Sat, 11 Dec 2021 06:43:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:43:10: #1 finished! INFO @ Sat, 11 Dec 2021 06:43:10: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:43:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:43:11: #2 number of paired peaks: 374 WARNING @ Sat, 11 Dec 2021 06:43:11: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Sat, 11 Dec 2021 06:43:11: start model_add_line... INFO @ Sat, 11 Dec 2021 06:43:11: start X-correlation... INFO @ Sat, 11 Dec 2021 06:43:11: end of X-cor INFO @ Sat, 11 Dec 2021 06:43:11: #2 finished! INFO @ Sat, 11 Dec 2021 06:43:11: #2 predicted fragment length is 49 bps INFO @ Sat, 11 Dec 2021 06:43:11: #2 alternative fragment length(s) may be 49 bps INFO @ Sat, 11 Dec 2021 06:43:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.20_model.r WARNING @ Sat, 11 Dec 2021 06:43:11: #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 06:43:11: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Sat, 11 Dec 2021 06:43:11: #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 06:43:11: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:43:11: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:43:23: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:43:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:43:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:43:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689011/SRX8689011.20_summits.bed INFO @ Sat, 11 Dec 2021 06:43:29: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (782 records, 4 fields): 2 millis CompletedMACS2peakCalling