Job ID = 14168012 SRX = SRX8688937 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: 00:10:29 23229247 reads; of these: 23229247 (100.00%) were unpaired; of these: 874585 (3.77%) aligned 0 times 15029631 (64.70%) aligned exactly 1 time 7325031 (31.53%) aligned >1 times 96.23% overall alignment rate Time searching: 00:10:29 Overall time: 00:10:29 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3721773 / 22354662 = 0.1665 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 14:38:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.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 14:38:00: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:38:00: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:38:11: 1000000 INFO @ Fri, 10 Dec 2021 14:38:21: 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 14:38:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.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 14:38:29: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:38:29: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:38:30: 3000000 INFO @ Fri, 10 Dec 2021 14:38:38: 1000000 INFO @ Fri, 10 Dec 2021 14:38:40: 4000000 INFO @ Fri, 10 Dec 2021 14:38:46: 2000000 INFO @ Fri, 10 Dec 2021 14:38:49: 5000000 INFO @ Fri, 10 Dec 2021 14:38:55: 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 @ Fri, 10 Dec 2021 14:38:59: 6000000 INFO @ Fri, 10 Dec 2021 14:38:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.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 14:38:59: #1 read tag files... INFO @ Fri, 10 Dec 2021 14:38:59: #1 read treatment tags... INFO @ Fri, 10 Dec 2021 14:39:03: 4000000 INFO @ Fri, 10 Dec 2021 14:39:09: 7000000 INFO @ Fri, 10 Dec 2021 14:39:09: 1000000 INFO @ Fri, 10 Dec 2021 14:39:11: 5000000 INFO @ Fri, 10 Dec 2021 14:39:18: 2000000 INFO @ Fri, 10 Dec 2021 14:39:19: 8000000 INFO @ Fri, 10 Dec 2021 14:39:20: 6000000 INFO @ Fri, 10 Dec 2021 14:39:27: 3000000 INFO @ Fri, 10 Dec 2021 14:39:28: 7000000 INFO @ Fri, 10 Dec 2021 14:39:28: 9000000 INFO @ Fri, 10 Dec 2021 14:39:36: 4000000 INFO @ Fri, 10 Dec 2021 14:39:36: 8000000 INFO @ Fri, 10 Dec 2021 14:39:38: 10000000 INFO @ Fri, 10 Dec 2021 14:39:45: 5000000 INFO @ Fri, 10 Dec 2021 14:39:45: 9000000 INFO @ Fri, 10 Dec 2021 14:39:48: 11000000 INFO @ Fri, 10 Dec 2021 14:39:53: 10000000 INFO @ Fri, 10 Dec 2021 14:39:53: 6000000 INFO @ Fri, 10 Dec 2021 14:39:58: 12000000 INFO @ Fri, 10 Dec 2021 14:40:01: 11000000 INFO @ Fri, 10 Dec 2021 14:40:02: 7000000 INFO @ Fri, 10 Dec 2021 14:40:08: 13000000 INFO @ Fri, 10 Dec 2021 14:40:10: 12000000 INFO @ Fri, 10 Dec 2021 14:40:10: 8000000 INFO @ Fri, 10 Dec 2021 14:40:18: 14000000 INFO @ Fri, 10 Dec 2021 14:40:19: 13000000 INFO @ Fri, 10 Dec 2021 14:40:19: 9000000 INFO @ Fri, 10 Dec 2021 14:40:27: 15000000 INFO @ Fri, 10 Dec 2021 14:40:27: 10000000 INFO @ Fri, 10 Dec 2021 14:40:27: 14000000 INFO @ Fri, 10 Dec 2021 14:40:36: 15000000 INFO @ Fri, 10 Dec 2021 14:40:36: 11000000 INFO @ Fri, 10 Dec 2021 14:40:38: 16000000 INFO @ Fri, 10 Dec 2021 14:40:44: 12000000 INFO @ Fri, 10 Dec 2021 14:40:45: 16000000 INFO @ Fri, 10 Dec 2021 14:40:48: 17000000 INFO @ Fri, 10 Dec 2021 14:40:53: 13000000 INFO @ Fri, 10 Dec 2021 14:40:55: 17000000 INFO @ Fri, 10 Dec 2021 14:40:57: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 10 Dec 2021 14:41:03: 14000000 INFO @ Fri, 10 Dec 2021 14:41:04: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:41:04: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:41:04: #1 total tags in treatment: 18632889 INFO @ Fri, 10 Dec 2021 14:41:04: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:41:04: #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 14:41:04: 18000000 INFO @ Fri, 10 Dec 2021 14:41:05: #1 tags after filtering in treatment: 18632889 INFO @ Fri, 10 Dec 2021 14:41:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:41:05: #1 finished! INFO @ Fri, 10 Dec 2021 14:41:05: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:41:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:41:06: #2 number of paired peaks: 285 WARNING @ Fri, 10 Dec 2021 14:41:06: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Fri, 10 Dec 2021 14:41:06: start model_add_line... INFO @ Fri, 10 Dec 2021 14:41:06: start X-correlation... INFO @ Fri, 10 Dec 2021 14:41:06: end of X-cor INFO @ Fri, 10 Dec 2021 14:41:06: #2 finished! INFO @ Fri, 10 Dec 2021 14:41:06: #2 predicted fragment length is 51 bps INFO @ Fri, 10 Dec 2021 14:41:06: #2 alternative fragment length(s) may be 4,51 bps INFO @ Fri, 10 Dec 2021 14:41:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.05_model.r WARNING @ Fri, 10 Dec 2021 14:41:06: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:41:06: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Fri, 10 Dec 2021 14:41:06: #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 14:41:06: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:41:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:41:10: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:41:10: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:41:10: #1 total tags in treatment: 18632889 INFO @ Fri, 10 Dec 2021 14:41:10: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:41:10: #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 14:41:11: #1 tags after filtering in treatment: 18632889 INFO @ Fri, 10 Dec 2021 14:41:11: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:41:11: #1 finished! INFO @ Fri, 10 Dec 2021 14:41:11: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:41:11: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:41:11: 15000000 INFO @ Fri, 10 Dec 2021 14:41:12: #2 number of paired peaks: 285 WARNING @ Fri, 10 Dec 2021 14:41:12: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Fri, 10 Dec 2021 14:41:12: start model_add_line... INFO @ Fri, 10 Dec 2021 14:41:12: start X-correlation... INFO @ Fri, 10 Dec 2021 14:41:12: end of X-cor INFO @ Fri, 10 Dec 2021 14:41:12: #2 finished! INFO @ Fri, 10 Dec 2021 14:41:12: #2 predicted fragment length is 51 bps INFO @ Fri, 10 Dec 2021 14:41:12: #2 alternative fragment length(s) may be 4,51 bps INFO @ Fri, 10 Dec 2021 14:41:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.10_model.r WARNING @ Fri, 10 Dec 2021 14:41:12: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:41:12: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Fri, 10 Dec 2021 14:41:12: #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 14:41:12: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:41:12: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:41:21: 16000000 INFO @ Fri, 10 Dec 2021 14:41:30: 17000000 INFO @ Fri, 10 Dec 2021 14:41:39: 18000000 INFO @ Fri, 10 Dec 2021 14:41:44: #1 tag size is determined as 50 bps INFO @ Fri, 10 Dec 2021 14:41:44: #1 tag size = 50 INFO @ Fri, 10 Dec 2021 14:41:44: #1 total tags in treatment: 18632889 INFO @ Fri, 10 Dec 2021 14:41:44: #1 user defined the maximum tags... INFO @ Fri, 10 Dec 2021 14:41:44: #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 14:41:45: #1 tags after filtering in treatment: 18632889 INFO @ Fri, 10 Dec 2021 14:41:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Dec 2021 14:41:45: #1 finished! INFO @ Fri, 10 Dec 2021 14:41:45: #2 Build Peak Model... INFO @ Fri, 10 Dec 2021 14:41:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Dec 2021 14:41:47: #2 number of paired peaks: 285 WARNING @ Fri, 10 Dec 2021 14:41:47: Fewer paired peaks (285) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 285 pairs to build model! INFO @ Fri, 10 Dec 2021 14:41:47: start model_add_line... INFO @ Fri, 10 Dec 2021 14:41:47: start X-correlation... INFO @ Fri, 10 Dec 2021 14:41:47: end of X-cor INFO @ Fri, 10 Dec 2021 14:41:47: #2 finished! INFO @ Fri, 10 Dec 2021 14:41:47: #2 predicted fragment length is 51 bps INFO @ Fri, 10 Dec 2021 14:41:47: #2 alternative fragment length(s) may be 4,51 bps INFO @ Fri, 10 Dec 2021 14:41:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.20_model.r WARNING @ Fri, 10 Dec 2021 14:41:47: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Dec 2021 14:41:47: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Fri, 10 Dec 2021 14:41:47: #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 14:41:47: #3 Call peaks... INFO @ Fri, 10 Dec 2021 14:41:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Dec 2021 14:41:57: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 10 Dec 2021 14:42:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:42:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.05_peaks.xls INFO @ Fri, 10 Dec 2021 14:42:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.05_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:42:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.05_summits.bed INFO @ Fri, 10 Dec 2021 14:42:22: Done! pass1 - making usageList (775 chroms): 2 millis pass2 - checking and writing primary data (3210 records, 4 fields): 90 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:42:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.10_peaks.xls INFO @ Fri, 10 Dec 2021 14:42:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.10_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:42:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.10_summits.bed INFO @ Fri, 10 Dec 2021 14:42:28: Done! pass1 - making usageList (489 chroms): 2 millis pass2 - checking and writing primary data (1487 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 10 Dec 2021 14:42:37: #3 Call peaks for each chromosome... INFO @ Fri, 10 Dec 2021 14:43:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.20_peaks.xls INFO @ Fri, 10 Dec 2021 14:43:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.20_peaks.narrowPeak INFO @ Fri, 10 Dec 2021 14:43:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX8688937/SRX8688937.20_summits.bed INFO @ Fri, 10 Dec 2021 14:43:00: Done! pass1 - making usageList (227 chroms): 1 millis pass2 - checking and writing primary data (461 records, 4 fields): 13 millis CompletedMACS2peakCalling