Job ID = 6498601 SRX = SRX645110 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:47:52 prefetch.2.10.7: 1) Downloading 'SRR1505709'... 2020-06-25T23:47:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:57:37 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:57:37 prefetch.2.10.7: 1) 'SRR1505709' was downloaded successfully Read 40000000 spots for SRR1505709/SRR1505709.sra Written 40000000 spots for SRR1505709/SRR1505709.sra 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: 00:16:13 40000000 reads; of these: 40000000 (100.00%) were unpaired; of these: 25112317 (62.78%) aligned 0 times 11256592 (28.14%) aligned exactly 1 time 3631091 (9.08%) aligned >1 times 37.22% overall alignment rate Time searching: 00:16:13 Overall time: 00:16:13 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 8 files... [bam_rmdupse_core] 8721646 / 14887683 = 0.5858 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 09:21:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.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, 26 Jun 2020 09:21:41: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:21:41: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:21:48: 1000000 INFO @ Fri, 26 Jun 2020 09:21:55: 2000000 INFO @ Fri, 26 Jun 2020 09:22:02: 3000000 INFO @ Fri, 26 Jun 2020 09:22:09: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 09:22:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.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, 26 Jun 2020 09:22:11: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:22:11: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:22:16: 5000000 INFO @ Fri, 26 Jun 2020 09:22:19: 1000000 INFO @ Fri, 26 Jun 2020 09:22:23: 6000000 INFO @ Fri, 26 Jun 2020 09:22:24: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:22:24: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:22:24: #1 total tags in treatment: 6166037 INFO @ Fri, 26 Jun 2020 09:22:24: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:22:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:22:25: #1 tags after filtering in treatment: 6166037 INFO @ Fri, 26 Jun 2020 09:22:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:22:25: #1 finished! INFO @ Fri, 26 Jun 2020 09:22:25: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:22:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:22:25: #2 number of paired peaks: 241 WARNING @ Fri, 26 Jun 2020 09:22:25: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Fri, 26 Jun 2020 09:22:25: start model_add_line... INFO @ Fri, 26 Jun 2020 09:22:25: start X-correlation... INFO @ Fri, 26 Jun 2020 09:22:25: end of X-cor INFO @ Fri, 26 Jun 2020 09:22:25: #2 finished! INFO @ Fri, 26 Jun 2020 09:22:25: #2 predicted fragment length is 83 bps INFO @ Fri, 26 Jun 2020 09:22:25: #2 alternative fragment length(s) may be 83 bps INFO @ Fri, 26 Jun 2020 09:22:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.05_model.r WARNING @ Fri, 26 Jun 2020 09:22:25: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:22:25: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Fri, 26 Jun 2020 09:22:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:22:25: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:22:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:22:26: 2000000 INFO @ Fri, 26 Jun 2020 09:22:34: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Fri, 26 Jun 2020 09:22:40: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:22:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.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, 26 Jun 2020 09:22:41: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:22:41: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:22:42: 4000000 INFO @ Fri, 26 Jun 2020 09:22:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:22:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:22:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.05_summits.bed INFO @ Fri, 26 Jun 2020 09:22:47: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2283 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:22:49: 1000000 INFO @ Fri, 26 Jun 2020 09:22:49: 5000000 INFO @ Fri, 26 Jun 2020 09:22:57: 2000000 INFO @ Fri, 26 Jun 2020 09:22:57: 6000000 INFO @ Fri, 26 Jun 2020 09:22:59: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:22:59: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:22:59: #1 total tags in treatment: 6166037 INFO @ Fri, 26 Jun 2020 09:22:59: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:22:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:22:59: #1 tags after filtering in treatment: 6166037 INFO @ Fri, 26 Jun 2020 09:22:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:22:59: #1 finished! INFO @ Fri, 26 Jun 2020 09:22:59: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:22:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:22:59: #2 number of paired peaks: 241 WARNING @ Fri, 26 Jun 2020 09:22:59: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Fri, 26 Jun 2020 09:22:59: start model_add_line... INFO @ Fri, 26 Jun 2020 09:22:59: start X-correlation... INFO @ Fri, 26 Jun 2020 09:22:59: end of X-cor INFO @ Fri, 26 Jun 2020 09:22:59: #2 finished! INFO @ Fri, 26 Jun 2020 09:22:59: #2 predicted fragment length is 83 bps INFO @ Fri, 26 Jun 2020 09:22:59: #2 alternative fragment length(s) may be 83 bps INFO @ Fri, 26 Jun 2020 09:22:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.10_model.r WARNING @ Fri, 26 Jun 2020 09:22:59: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:22:59: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Fri, 26 Jun 2020 09:22:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:22:59: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:22:59: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:23:04: 3000000 INFO @ Fri, 26 Jun 2020 09:23:12: 4000000 INFO @ Fri, 26 Jun 2020 09:23:14: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:23:19: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:23:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:23:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:23:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.10_summits.bed INFO @ Fri, 26 Jun 2020 09:23:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1077 records, 4 fields): 85 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 09:23:26: 6000000 INFO @ Fri, 26 Jun 2020 09:23:27: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 09:23:27: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 09:23:27: #1 total tags in treatment: 6166037 INFO @ Fri, 26 Jun 2020 09:23:27: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:23:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 09:23:27: #1 tags after filtering in treatment: 6166037 INFO @ Fri, 26 Jun 2020 09:23:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:23:27: #1 finished! INFO @ Fri, 26 Jun 2020 09:23:27: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:23:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:23:28: #2 number of paired peaks: 241 WARNING @ Fri, 26 Jun 2020 09:23:28: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Fri, 26 Jun 2020 09:23:28: start model_add_line... INFO @ Fri, 26 Jun 2020 09:23:28: start X-correlation... INFO @ Fri, 26 Jun 2020 09:23:28: end of X-cor INFO @ Fri, 26 Jun 2020 09:23:28: #2 finished! INFO @ Fri, 26 Jun 2020 09:23:28: #2 predicted fragment length is 83 bps INFO @ Fri, 26 Jun 2020 09:23:28: #2 alternative fragment length(s) may be 83 bps INFO @ Fri, 26 Jun 2020 09:23:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.20_model.r WARNING @ Fri, 26 Jun 2020 09:23:28: #2 Since the d (83) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:23:28: #2 You may need to consider one of the other alternative d(s): 83 WARNING @ Fri, 26 Jun 2020 09:23:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 09:23:28: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:23:28: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:23:42: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:23:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:23:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:23:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645110/SRX645110.20_summits.bed INFO @ Fri, 26 Jun 2020 09:23:49: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (654 records, 4 fields): 2 millis CompletedMACS2peakCalling