Job ID = 14170377 SRX = SRX8689001 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 21409872 spots for SRR12174232/SRR12174232.sra Written 21409872 spots for SRR12174232/SRR12174232.sra fastq に変換しました。 bowtie でマッピング中... Your job 14170784 ("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: 00:09:37 21409872 reads; of these: 21409872 (100.00%) were unpaired; of these: 594583 (2.78%) aligned 0 times 14663749 (68.49%) aligned exactly 1 time 6151540 (28.73%) aligned >1 times 97.22% overall alignment rate Time searching: 00:09:37 Overall time: 00:09:37 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 12 files... [bam_rmdupse_core] 1976825 / 20815289 = 0.0950 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 06:43:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.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 06:43:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:43:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:43:55: 1000000 INFO @ Sat, 11 Dec 2021 06:44:06: 2000000 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 06:44:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.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 06:44:14: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:44:14: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:44:16: 3000000 INFO @ Sat, 11 Dec 2021 06:44:23: 1000000 INFO @ Sat, 11 Dec 2021 06:44:27: 4000000 INFO @ Sat, 11 Dec 2021 06:44:31: 2000000 INFO @ Sat, 11 Dec 2021 06:44:38: 5000000 INFO @ Sat, 11 Dec 2021 06:44:40: 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 06:44:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.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 06:44:44: #1 read tag files... INFO @ Sat, 11 Dec 2021 06:44:44: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 06:44:48: 4000000 INFO @ Sat, 11 Dec 2021 06:44:49: 6000000 INFO @ Sat, 11 Dec 2021 06:44:54: 1000000 INFO @ Sat, 11 Dec 2021 06:44:56: 5000000 INFO @ Sat, 11 Dec 2021 06:45:00: 7000000 INFO @ Sat, 11 Dec 2021 06:45:04: 2000000 INFO @ Sat, 11 Dec 2021 06:45:04: 6000000 INFO @ Sat, 11 Dec 2021 06:45:11: 8000000 INFO @ Sat, 11 Dec 2021 06:45:13: 7000000 INFO @ Sat, 11 Dec 2021 06:45:14: 3000000 INFO @ Sat, 11 Dec 2021 06:45:22: 9000000 INFO @ Sat, 11 Dec 2021 06:45:22: 8000000 INFO @ Sat, 11 Dec 2021 06:45:24: 4000000 INFO @ Sat, 11 Dec 2021 06:45:32: 9000000 INFO @ Sat, 11 Dec 2021 06:45:33: 10000000 INFO @ Sat, 11 Dec 2021 06:45:35: 5000000 INFO @ Sat, 11 Dec 2021 06:45:41: 10000000 INFO @ Sat, 11 Dec 2021 06:45:44: 11000000 INFO @ Sat, 11 Dec 2021 06:45:45: 6000000 INFO @ Sat, 11 Dec 2021 06:45:51: 11000000 INFO @ Sat, 11 Dec 2021 06:45:56: 7000000 INFO @ Sat, 11 Dec 2021 06:45:56: 12000000 INFO @ Sat, 11 Dec 2021 06:46:00: 12000000 INFO @ Sat, 11 Dec 2021 06:46:06: 8000000 INFO @ Sat, 11 Dec 2021 06:46:08: 13000000 INFO @ Sat, 11 Dec 2021 06:46:10: 13000000 INFO @ Sat, 11 Dec 2021 06:46:17: 9000000 INFO @ Sat, 11 Dec 2021 06:46:20: 14000000 INFO @ Sat, 11 Dec 2021 06:46:20: 14000000 INFO @ Sat, 11 Dec 2021 06:46:28: 10000000 INFO @ Sat, 11 Dec 2021 06:46:31: 15000000 INFO @ Sat, 11 Dec 2021 06:46:32: 15000000 INFO @ Sat, 11 Dec 2021 06:46:39: 11000000 INFO @ Sat, 11 Dec 2021 06:46:41: 16000000 INFO @ Sat, 11 Dec 2021 06:46:44: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 06:46:50: 12000000 INFO @ Sat, 11 Dec 2021 06:46:52: 17000000 INFO @ Sat, 11 Dec 2021 06:46:55: 17000000 INFO @ Sat, 11 Dec 2021 06:47:01: 13000000 INFO @ Sat, 11 Dec 2021 06:47:02: 18000000 INFO @ Sat, 11 Dec 2021 06:47:06: 18000000 INFO @ Sat, 11 Dec 2021 06:47:11: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:47:11: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:47:11: #1 total tags in treatment: 18838464 INFO @ Sat, 11 Dec 2021 06:47:11: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:47:11: #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 06:47:11: #1 tags after filtering in treatment: 18838464 INFO @ Sat, 11 Dec 2021 06:47:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:47:11: #1 finished! INFO @ Sat, 11 Dec 2021 06:47:11: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:47:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:47:12: 14000000 INFO @ Sat, 11 Dec 2021 06:47:13: #2 number of paired peaks: 112 WARNING @ Sat, 11 Dec 2021 06:47:13: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 11 Dec 2021 06:47:13: start model_add_line... INFO @ Sat, 11 Dec 2021 06:47:13: start X-correlation... INFO @ Sat, 11 Dec 2021 06:47:13: end of X-cor INFO @ Sat, 11 Dec 2021 06:47:13: #2 finished! INFO @ Sat, 11 Dec 2021 06:47:13: #2 predicted fragment length is 45 bps INFO @ Sat, 11 Dec 2021 06:47:13: #2 alternative fragment length(s) may be 45 bps INFO @ Sat, 11 Dec 2021 06:47:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.10_model.r WARNING @ Sat, 11 Dec 2021 06:47:13: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:47:13: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sat, 11 Dec 2021 06:47:13: #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 06:47:13: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:47:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:47:15: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:47:15: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:47:15: #1 total tags in treatment: 18838464 INFO @ Sat, 11 Dec 2021 06:47:15: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:47:15: #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 06:47:16: #1 tags after filtering in treatment: 18838464 INFO @ Sat, 11 Dec 2021 06:47:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:47:16: #1 finished! INFO @ Sat, 11 Dec 2021 06:47:16: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:47:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:47:17: #2 number of paired peaks: 112 WARNING @ Sat, 11 Dec 2021 06:47:17: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 11 Dec 2021 06:47:17: start model_add_line... INFO @ Sat, 11 Dec 2021 06:47:17: start X-correlation... INFO @ Sat, 11 Dec 2021 06:47:17: end of X-cor INFO @ Sat, 11 Dec 2021 06:47:17: #2 finished! INFO @ Sat, 11 Dec 2021 06:47:17: #2 predicted fragment length is 45 bps INFO @ Sat, 11 Dec 2021 06:47:17: #2 alternative fragment length(s) may be 45 bps INFO @ Sat, 11 Dec 2021 06:47:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.05_model.r WARNING @ Sat, 11 Dec 2021 06:47:17: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:47:17: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sat, 11 Dec 2021 06:47:17: #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 06:47:17: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:47:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:47:22: 15000000 INFO @ Sat, 11 Dec 2021 06:47:32: 16000000 INFO @ Sat, 11 Dec 2021 06:47:42: 17000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 06:47:52: 18000000 INFO @ Sat, 11 Dec 2021 06:48:01: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 06:48:01: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 06:48:01: #1 total tags in treatment: 18838464 INFO @ Sat, 11 Dec 2021 06:48:01: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 06:48:01: #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 06:48:01: #1 tags after filtering in treatment: 18838464 INFO @ Sat, 11 Dec 2021 06:48:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 06:48:01: #1 finished! INFO @ Sat, 11 Dec 2021 06:48:01: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 06:48:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 06:48:01: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:48:03: #2 number of paired peaks: 112 WARNING @ Sat, 11 Dec 2021 06:48:03: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Sat, 11 Dec 2021 06:48:03: start model_add_line... INFO @ Sat, 11 Dec 2021 06:48:03: start X-correlation... INFO @ Sat, 11 Dec 2021 06:48:03: end of X-cor INFO @ Sat, 11 Dec 2021 06:48:03: #2 finished! INFO @ Sat, 11 Dec 2021 06:48:03: #2 predicted fragment length is 45 bps INFO @ Sat, 11 Dec 2021 06:48:03: #2 alternative fragment length(s) may be 45 bps INFO @ Sat, 11 Dec 2021 06:48:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.20_model.r WARNING @ Sat, 11 Dec 2021 06:48:03: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 06:48:03: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Sat, 11 Dec 2021 06:48:03: #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 06:48:03: #3 Call peaks... INFO @ Sat, 11 Dec 2021 06:48:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 06:48:05: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:48:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.10_peaks.xls INFO @ Sat, 11 Dec 2021 06:48:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:48:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.10_summits.bed INFO @ Sat, 11 Dec 2021 06:48:25: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1407 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:48:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.05_peaks.xls INFO @ Sat, 11 Dec 2021 06:48:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:48:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.05_summits.bed INFO @ Sat, 11 Dec 2021 06:48:28: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1854 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 06:48:52: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 06:49:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.20_peaks.xls INFO @ Sat, 11 Dec 2021 06:49:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 06:49:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8689001/SRX8689001.20_summits.bed INFO @ Sat, 11 Dec 2021 06:49:16: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1081 records, 4 fields): 6 millis CompletedMACS2peakCalling