Job ID = 14167096 SRX = SRX7723698 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 22379588 spots for SRR11084654/SRR11084654.sra Written 22379588 spots for SRR11084654/SRR11084654.sra fastq に変換しました。 bowtie でマッピング中... Your job 14167528 ("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: 00:12:29 22379588 reads; of these: 22379588 (100.00%) were unpaired; of these: 1784453 (7.97%) aligned 0 times 14392056 (64.31%) aligned exactly 1 time 6203079 (27.72%) aligned >1 times 92.03% overall alignment rate Time searching: 00:12:29 Overall time: 00:12:29 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] 5148255 / 20595135 = 0.2500 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 10:10:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.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 10:10:09: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:10:09: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:10:20: 1000000 INFO @ Fri, 10 Dec 2021 10:10:30: 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 @ Fri, 10 Dec 2021 10:10:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.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 10:10:39: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:10:39: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:10:41: 3000000 INFO @ Fri, 10 Dec 2021 10:10:51: 1000000 INFO @ Fri, 10 Dec 2021 10:10:52: 4000000 INFO @ Fri, 10 Dec 2021 10:11:03: 2000000 INFO @ Fri, 10 Dec 2021 10:11:03: 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 @ Fri, 10 Dec 2021 10:11:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.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 10:11:09: #1 read tag files... INFO @ Fri, 10 Dec 2021 10:11:09: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 10:11:15: 3000000 INFO @ Fri, 10 Dec 2021 10:11:15: 6000000 INFO @ Fri, 10 Dec 2021 10:11:24: 1000000 INFO @ Fri, 10 Dec 2021 10:11:27: 4000000 INFO @ Fri, 10 Dec 2021 10:11:27: 7000000 INFO @ Fri, 10 Dec 2021 10:11:38: 8000000 INFO @ Fri, 10 Dec 2021 10:11:38: 5000000 INFO @ Fri, 10 Dec 2021 10:11:38: 2000000 INFO @ Fri, 10 Dec 2021 10:11:48: 9000000 INFO @ Fri, 10 Dec 2021 10:11:49: 6000000 INFO @ Fri, 10 Dec 2021 10:11:52: 3000000 INFO @ Fri, 10 Dec 2021 10:11:59: 10000000 INFO @ Fri, 10 Dec 2021 10:12:01: 7000000 INFO @ Fri, 10 Dec 2021 10:12:06: 4000000 INFO @ Fri, 10 Dec 2021 10:12:10: 11000000 INFO @ Fri, 10 Dec 2021 10:12:12: 8000000 INFO @ Fri, 10 Dec 2021 10:12:20: 12000000 INFO @ Fri, 10 Dec 2021 10:12:21: 5000000 INFO @ Fri, 10 Dec 2021 10:12:24: 9000000 INFO @ Fri, 10 Dec 2021 10:12:31: 13000000 INFO @ Fri, 10 Dec 2021 10:12:35: 10000000 INFO @ Fri, 10 Dec 2021 10:12:35: 6000000 INFO @ Fri, 10 Dec 2021 10:12:42: 14000000 INFO @ Fri, 10 Dec 2021 10:12:46: 11000000 INFO @ Fri, 10 Dec 2021 10:12:48: 7000000 INFO @ Fri, 10 Dec 2021 10:12:52: 15000000 INFO @ Fri, 10 Dec 2021 10:12:56: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 10:12:56: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 10:12:56: #1 total tags in treatment: 15446880 INFO @ Fri, 10 Dec 2021 10:12:56: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:12:56: #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 10:12:56: #1 tags after filtering in treatment: 15446880 INFO @ Fri, 10 Dec 2021 10:12:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:12:56: #1 finished! INFO @ Fri, 10 Dec 2021 10:12:56: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:12:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:12:57: 12000000 INFO @ Fri, 10 Dec 2021 10:12:58: #2 number of paired peaks: 452 WARNING @ Fri, 10 Dec 2021 10:12:58: Fewer paired peaks (452) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 452 pairs to build model! INFO @ Fri, 10 Dec 2021 10:12:58: start model_add_line... INFO @ Fri, 10 Dec 2021 10:12:58: start X-correlation... INFO @ Fri, 10 Dec 2021 10:12:58: end of X-cor INFO @ Fri, 10 Dec 2021 10:12:58: #2 finished! INFO @ Fri, 10 Dec 2021 10:12:58: #2 predicted fragment length is 64 bps INFO @ Fri, 10 Dec 2021 10:12:58: #2 alternative fragment length(s) may be 64 bps INFO @ Fri, 10 Dec 2021 10:12:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.05_model.r WARNING @ Fri, 10 Dec 2021 10:12:58: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:12:58: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Fri, 10 Dec 2021 10:12:58: #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 10:12:58: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:12:58: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 10:13:02: 8000000 INFO @ Fri, 10 Dec 2021 10:13:08: 13000000 INFO @ Fri, 10 Dec 2021 10:13:16: 9000000 INFO @ Fri, 10 Dec 2021 10:13:18: 14000000 INFO @ Fri, 10 Dec 2021 10:13:29: 15000000 INFO @ Fri, 10 Dec 2021 10:13:30: 10000000 INFO @ Fri, 10 Dec 2021 10:13:33: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 10:13:33: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 10:13:33: #1 total tags in treatment: 15446880 INFO @ Fri, 10 Dec 2021 10:13:33: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:13:33: #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 10:13:33: #1 tags after filtering in treatment: 15446880 INFO @ Fri, 10 Dec 2021 10:13:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:13:33: #1 finished! INFO @ Fri, 10 Dec 2021 10:13:33: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:13:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:13:35: #2 number of paired peaks: 452 WARNING @ Fri, 10 Dec 2021 10:13:35: Fewer paired peaks (452) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 452 pairs to build model! INFO @ Fri, 10 Dec 2021 10:13:35: start model_add_line... INFO @ Fri, 10 Dec 2021 10:13:35: start X-correlation... INFO @ Fri, 10 Dec 2021 10:13:35: end of X-cor INFO @ Fri, 10 Dec 2021 10:13:35: #2 finished! INFO @ Fri, 10 Dec 2021 10:13:35: #2 predicted fragment length is 64 bps INFO @ Fri, 10 Dec 2021 10:13:35: #2 alternative fragment length(s) may be 64 bps INFO @ Fri, 10 Dec 2021 10:13:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.10_model.r WARNING @ Fri, 10 Dec 2021 10:13:35: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:13:35: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Fri, 10 Dec 2021 10:13:35: #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 10:13:35: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:13:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:13:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:13:43: 11000000 BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 10:13:55: 12000000 INFO @ Fri, 10 Dec 2021 10:14:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.05_peaks.xls INFO @ Fri, 10 Dec 2021 10:14:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:14:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.05_summits.bed INFO @ Fri, 10 Dec 2021 10:14:03: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8287 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:14:08: 13000000 INFO @ Fri, 10 Dec 2021 10:14:17: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:14:21: 14000000 INFO @ Fri, 10 Dec 2021 10:14:33: 15000000 INFO @ Fri, 10 Dec 2021 10:14:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.10_peaks.xls INFO @ Fri, 10 Dec 2021 10:14:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:14:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.10_summits.bed INFO @ Fri, 10 Dec 2021 10:14:38: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3955 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 10:14:38: #1 tag size is determined as 75 bps INFO @ Fri, 10 Dec 2021 10:14:38: #1 tag size = 75 INFO @ Fri, 10 Dec 2021 10:14:38: #1 total tags in treatment: 15446880 INFO @ Fri, 10 Dec 2021 10:14:38: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 10:14:38: #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 10:14:39: #1 tags after filtering in treatment: 15446880 INFO @ Fri, 10 Dec 2021 10:14:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 10:14:39: #1 finished! INFO @ Fri, 10 Dec 2021 10:14:39: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 10:14:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 10:14:40: #2 number of paired peaks: 452 WARNING @ Fri, 10 Dec 2021 10:14:40: Fewer paired peaks (452) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 452 pairs to build model! INFO @ Fri, 10 Dec 2021 10:14:40: start model_add_line... INFO @ Fri, 10 Dec 2021 10:14:40: start X-correlation... INFO @ Fri, 10 Dec 2021 10:14:40: end of X-cor INFO @ Fri, 10 Dec 2021 10:14:40: #2 finished! INFO @ Fri, 10 Dec 2021 10:14:40: #2 predicted fragment length is 64 bps INFO @ Fri, 10 Dec 2021 10:14:40: #2 alternative fragment length(s) may be 64 bps INFO @ Fri, 10 Dec 2021 10:14:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.20_model.r WARNING @ Fri, 10 Dec 2021 10:14:40: #2 Since the d (64) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 10:14:40: #2 You may need to consider one of the other alternative d(s): 64 WARNING @ Fri, 10 Dec 2021 10:14:40: #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 10:14:40: #3 Call peaks... INFO @ Fri, 10 Dec 2021 10:14:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 10:15:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 10:15:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.20_peaks.xls INFO @ Fri, 10 Dec 2021 10:15:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 10:15:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX7723698/SRX7723698.20_summits.bed INFO @ Fri, 10 Dec 2021 10:15:42: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1261 records, 4 fields): 6 millis CompletedMACS2peakCalling