Job ID = 14170792 SRX = SRX8689007 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:21 20333018 reads; of these: 20333018 (100.00%) were unpaired; of these: 666192 (3.28%) aligned 0 times 13362833 (65.72%) aligned exactly 1 time 6303993 (31.00%) aligned >1 times 96.72% overall alignment rate Time searching: 00:06:21 Overall time: 00:06:21 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 2821830 / 19666826 = 0.1435 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 08:53:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.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 08:53:58: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:53:58: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:54:04: 1000000 INFO @ Sat, 11 Dec 2021 08:54:10: 2000000 INFO @ Sat, 11 Dec 2021 08:54:15: 3000000 INFO @ Sat, 11 Dec 2021 08:54:21: 4000000 INFO @ Sat, 11 Dec 2021 08:54:26: 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 08:54:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.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 08:54:28: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:54:28: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:54:33: 6000000 INFO @ Sat, 11 Dec 2021 08:54:35: 1000000 INFO @ Sat, 11 Dec 2021 08:54:39: 7000000 INFO @ Sat, 11 Dec 2021 08:54:42: 2000000 INFO @ Sat, 11 Dec 2021 08:54:46: 8000000 INFO @ Sat, 11 Dec 2021 08:54:48: 3000000 INFO @ Sat, 11 Dec 2021 08:54:52: 9000000 INFO @ Sat, 11 Dec 2021 08:54:55: 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 @ Sat, 11 Dec 2021 08:54:59: 10000000 INFO @ Sat, 11 Dec 2021 08:55:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.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 08:55:01: #1 read tag files... INFO @ Sat, 11 Dec 2021 08:55:01: #1 read treatment tags... INFO @ Sat, 11 Dec 2021 08:55:02: 5000000 INFO @ Sat, 11 Dec 2021 08:55:06: 11000000 INFO @ Sat, 11 Dec 2021 08:55:09: 6000000 INFO @ Sat, 11 Dec 2021 08:55:09: 1000000 INFO @ Sat, 11 Dec 2021 08:55:13: 12000000 INFO @ Sat, 11 Dec 2021 08:55:16: 7000000 INFO @ Sat, 11 Dec 2021 08:55:17: 2000000 INFO @ Sat, 11 Dec 2021 08:55:20: 13000000 INFO @ Sat, 11 Dec 2021 08:55:23: 8000000 INFO @ Sat, 11 Dec 2021 08:55:25: 3000000 INFO @ Sat, 11 Dec 2021 08:55:28: 14000000 INFO @ Sat, 11 Dec 2021 08:55:30: 9000000 INFO @ Sat, 11 Dec 2021 08:55:33: 4000000 INFO @ Sat, 11 Dec 2021 08:55:35: 15000000 INFO @ Sat, 11 Dec 2021 08:55:37: 10000000 INFO @ Sat, 11 Dec 2021 08:55:41: 5000000 INFO @ Sat, 11 Dec 2021 08:55:42: 16000000 INFO @ Sat, 11 Dec 2021 08:55:45: 11000000 INFO @ Sat, 11 Dec 2021 08:55:49: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:55:49: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:55:49: #1 total tags in treatment: 16844996 INFO @ Sat, 11 Dec 2021 08:55:49: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:55:49: #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 08:55:49: #1 tags after filtering in treatment: 16844995 INFO @ Sat, 11 Dec 2021 08:55:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:55:49: #1 finished! INFO @ Sat, 11 Dec 2021 08:55:49: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:55:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:55:50: 6000000 INFO @ Sat, 11 Dec 2021 08:55:50: #2 number of paired peaks: 424 WARNING @ Sat, 11 Dec 2021 08:55:50: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Sat, 11 Dec 2021 08:55:50: start model_add_line... INFO @ Sat, 11 Dec 2021 08:55:51: start X-correlation... INFO @ Sat, 11 Dec 2021 08:55:51: end of X-cor INFO @ Sat, 11 Dec 2021 08:55:51: #2 finished! INFO @ Sat, 11 Dec 2021 08:55:51: #2 predicted fragment length is 58 bps INFO @ Sat, 11 Dec 2021 08:55:51: #2 alternative fragment length(s) may be 4,58 bps INFO @ Sat, 11 Dec 2021 08:55:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.05_model.r WARNING @ Sat, 11 Dec 2021 08:55:51: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:55:51: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Sat, 11 Dec 2021 08:55:51: #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 08:55:51: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:55:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:55:52: 12000000 INFO @ Sat, 11 Dec 2021 08:55:58: 7000000 INFO @ Sat, 11 Dec 2021 08:55:59: 13000000 INFO @ Sat, 11 Dec 2021 08:56:06: 8000000 INFO @ Sat, 11 Dec 2021 08:56:06: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 11 Dec 2021 08:56:14: 15000000 INFO @ Sat, 11 Dec 2021 08:56:14: 9000000 INFO @ Sat, 11 Dec 2021 08:56:20: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:56:21: 16000000 INFO @ Sat, 11 Dec 2021 08:56:22: 10000000 INFO @ Sat, 11 Dec 2021 08:56:27: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:56:27: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:56:27: #1 total tags in treatment: 16844996 INFO @ Sat, 11 Dec 2021 08:56:27: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:56:27: #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 08:56:28: #1 tags after filtering in treatment: 16844995 INFO @ Sat, 11 Dec 2021 08:56:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:56:28: #1 finished! INFO @ Sat, 11 Dec 2021 08:56:28: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:56:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:56:29: #2 number of paired peaks: 424 WARNING @ Sat, 11 Dec 2021 08:56:29: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Sat, 11 Dec 2021 08:56:29: start model_add_line... INFO @ Sat, 11 Dec 2021 08:56:29: start X-correlation... INFO @ Sat, 11 Dec 2021 08:56:29: end of X-cor INFO @ Sat, 11 Dec 2021 08:56:29: #2 finished! INFO @ Sat, 11 Dec 2021 08:56:29: #2 predicted fragment length is 58 bps INFO @ Sat, 11 Dec 2021 08:56:29: #2 alternative fragment length(s) may be 4,58 bps INFO @ Sat, 11 Dec 2021 08:56:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.10_model.r WARNING @ Sat, 11 Dec 2021 08:56:29: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:56:29: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Sat, 11 Dec 2021 08:56:29: #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 08:56:29: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:56:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:56:30: 11000000 INFO @ Sat, 11 Dec 2021 08:56:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.05_peaks.xls INFO @ Sat, 11 Dec 2021 08:56:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.05_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:56:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.05_summits.bed INFO @ Sat, 11 Dec 2021 08:56:35: Done! pass1 - making usageList (877 chroms): 1 millis pass2 - checking and writing primary data (3863 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:56:37: 12000000 INFO @ Sat, 11 Dec 2021 08:56:44: 13000000 BigWig に変換しました。 INFO @ Sat, 11 Dec 2021 08:56:52: 14000000 INFO @ Sat, 11 Dec 2021 08:56:59: 15000000 INFO @ Sat, 11 Dec 2021 08:57:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:57:06: 16000000 INFO @ Sat, 11 Dec 2021 08:57:12: #1 tag size is determined as 50 bps INFO @ Sat, 11 Dec 2021 08:57:12: #1 tag size = 50 INFO @ Sat, 11 Dec 2021 08:57:12: #1 total tags in treatment: 16844996 INFO @ Sat, 11 Dec 2021 08:57:12: #1 user defined the maximum tags... INFO @ Sat, 11 Dec 2021 08:57:12: #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 08:57:13: #1 tags after filtering in treatment: 16844995 INFO @ Sat, 11 Dec 2021 08:57:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Dec 2021 08:57:13: #1 finished! INFO @ Sat, 11 Dec 2021 08:57:13: #2 Build Peak Model... INFO @ Sat, 11 Dec 2021 08:57:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Dec 2021 08:57:14: #2 number of paired peaks: 424 WARNING @ Sat, 11 Dec 2021 08:57:14: Fewer paired peaks (424) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 424 pairs to build model! INFO @ Sat, 11 Dec 2021 08:57:14: start model_add_line... INFO @ Sat, 11 Dec 2021 08:57:14: start X-correlation... INFO @ Sat, 11 Dec 2021 08:57:14: end of X-cor INFO @ Sat, 11 Dec 2021 08:57:14: #2 finished! INFO @ Sat, 11 Dec 2021 08:57:14: #2 predicted fragment length is 58 bps INFO @ Sat, 11 Dec 2021 08:57:14: #2 alternative fragment length(s) may be 4,58 bps INFO @ Sat, 11 Dec 2021 08:57:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.20_model.r WARNING @ Sat, 11 Dec 2021 08:57:14: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Dec 2021 08:57:14: #2 You may need to consider one of the other alternative d(s): 4,58 WARNING @ Sat, 11 Dec 2021 08:57:14: #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 08:57:14: #3 Call peaks... INFO @ Sat, 11 Dec 2021 08:57:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Dec 2021 08:57:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.10_peaks.xls INFO @ Sat, 11 Dec 2021 08:57:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.10_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:57:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.10_summits.bed INFO @ Sat, 11 Dec 2021 08:57:15: Done! pass1 - making usageList (544 chroms): 1 millis pass2 - checking and writing primary data (1673 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 11 Dec 2021 08:57:45: #3 Call peaks for each chromosome... INFO @ Sat, 11 Dec 2021 08:58:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.20_peaks.xls INFO @ Sat, 11 Dec 2021 08:58:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.20_peaks.narrowPeak INFO @ Sat, 11 Dec 2021 08:58:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8689007/SRX8689007.20_summits.bed INFO @ Sat, 11 Dec 2021 08:58:00: Done! pass1 - making usageList (317 chroms): 1 millis pass2 - checking and writing primary data (673 records, 4 fields): 10 millis CompletedMACS2peakCalling