Job ID = 6527465 SRX = SRX016169 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:47:07 prefetch.2.10.7: 1) Downloading 'SRR034737'... 2020-06-29T12:47:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:49:04 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:49:04 prefetch.2.10.7: 'SRR034737' is valid 2020-06-29T12:49:04 prefetch.2.10.7: 1) 'SRR034737' was downloaded successfully Read 13718156 spots for SRR034737/SRR034737.sra Written 13718156 spots for SRR034737/SRR034737.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: 00:03:12 13718156 reads; of these: 13718156 (100.00%) were unpaired; of these: 1365320 (9.95%) aligned 0 times 10196271 (74.33%) aligned exactly 1 time 2156565 (15.72%) aligned >1 times 90.05% overall alignment rate Time searching: 00:03:12 Overall time: 00:03:12 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_rmdupse_core] 1898825 / 12352836 = 0.1537 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 @ Mon, 29 Jun 2020 21:58:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.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 @ Mon, 29 Jun 2020 21:58:59: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:58:59: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:59:04: 1000000 INFO @ Mon, 29 Jun 2020 21:59:09: 2000000 INFO @ Mon, 29 Jun 2020 21:59:14: 3000000 INFO @ Mon, 29 Jun 2020 21:59:19: 4000000 INFO @ Mon, 29 Jun 2020 21:59:24: 5000000 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 @ Mon, 29 Jun 2020 21:59:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.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 @ Mon, 29 Jun 2020 21:59:29: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:59:29: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:59:29: 6000000 INFO @ Mon, 29 Jun 2020 21:59:34: 1000000 INFO @ Mon, 29 Jun 2020 21:59:34: 7000000 INFO @ Mon, 29 Jun 2020 21:59:40: 8000000 INFO @ Mon, 29 Jun 2020 21:59:40: 2000000 INFO @ Mon, 29 Jun 2020 21:59:45: 9000000 INFO @ Mon, 29 Jun 2020 21:59:46: 3000000 INFO @ Mon, 29 Jun 2020 21:59:50: 10000000 INFO @ Mon, 29 Jun 2020 21:59:51: 4000000 INFO @ Mon, 29 Jun 2020 21:59:53: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 21:59:53: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 21:59:53: #1 total tags in treatment: 10454011 INFO @ Mon, 29 Jun 2020 21:59:53: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:59:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 21:59:53: #1 tags after filtering in treatment: 10454011 INFO @ Mon, 29 Jun 2020 21:59:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:59:53: #1 finished! INFO @ Mon, 29 Jun 2020 21:59:53: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:59:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:59:54: #2 number of paired peaks: 146 WARNING @ Mon, 29 Jun 2020 21:59:54: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Mon, 29 Jun 2020 21:59:54: start model_add_line... INFO @ Mon, 29 Jun 2020 21:59:54: start X-correlation... INFO @ Mon, 29 Jun 2020 21:59:54: end of X-cor INFO @ Mon, 29 Jun 2020 21:59:54: #2 finished! INFO @ Mon, 29 Jun 2020 21:59:54: #2 predicted fragment length is 35 bps INFO @ Mon, 29 Jun 2020 21:59:54: #2 alternative fragment length(s) may be 35 bps INFO @ Mon, 29 Jun 2020 21:59:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.05_model.r WARNING @ Mon, 29 Jun 2020 21:59:54: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:59:54: #2 You may need to consider one of the other alternative d(s): 35 WARNING @ Mon, 29 Jun 2020 21:59:54: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 21:59:54: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:59:54: #3 Pre-compute pvalue-qvalue table... 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 @ Mon, 29 Jun 2020 21:59:57: 5000000 INFO @ Mon, 29 Jun 2020 21:59:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.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 @ Mon, 29 Jun 2020 21:59:59: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:59:59: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:00:03: 6000000 INFO @ Mon, 29 Jun 2020 22:00:05: 1000000 INFO @ Mon, 29 Jun 2020 22:00:08: 7000000 INFO @ Mon, 29 Jun 2020 22:00:10: 2000000 INFO @ Mon, 29 Jun 2020 22:00:14: 8000000 INFO @ Mon, 29 Jun 2020 22:00:16: 3000000 INFO @ Mon, 29 Jun 2020 22:00:17: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:00:20: 9000000 INFO @ Mon, 29 Jun 2020 22:00:21: 4000000 INFO @ Mon, 29 Jun 2020 22:00:25: 10000000 INFO @ Mon, 29 Jun 2020 22:00:27: 5000000 INFO @ Mon, 29 Jun 2020 22:00:28: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:00:28: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:00:28: #1 total tags in treatment: 10454011 INFO @ Mon, 29 Jun 2020 22:00:28: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:00:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:00:28: #1 tags after filtering in treatment: 10454011 INFO @ Mon, 29 Jun 2020 22:00:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:00:28: #1 finished! INFO @ Mon, 29 Jun 2020 22:00:28: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:00:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:00:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:00:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:00:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.05_summits.bed INFO @ Mon, 29 Jun 2020 22:00:29: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1131 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:00:29: #2 number of paired peaks: 146 WARNING @ Mon, 29 Jun 2020 22:00:29: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Mon, 29 Jun 2020 22:00:29: start model_add_line... INFO @ Mon, 29 Jun 2020 22:00:29: start X-correlation... INFO @ Mon, 29 Jun 2020 22:00:29: end of X-cor INFO @ Mon, 29 Jun 2020 22:00:29: #2 finished! INFO @ Mon, 29 Jun 2020 22:00:29: #2 predicted fragment length is 35 bps INFO @ Mon, 29 Jun 2020 22:00:29: #2 alternative fragment length(s) may be 35 bps INFO @ Mon, 29 Jun 2020 22:00:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.10_model.r WARNING @ Mon, 29 Jun 2020 22:00:29: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:00:29: #2 You may need to consider one of the other alternative d(s): 35 WARNING @ Mon, 29 Jun 2020 22:00:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:00:29: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:00:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:00:32: 6000000 INFO @ Mon, 29 Jun 2020 22:00:37: 7000000 INFO @ Mon, 29 Jun 2020 22:00:42: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:00:48: 9000000 INFO @ Mon, 29 Jun 2020 22:00:51: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:00:53: 10000000 INFO @ Mon, 29 Jun 2020 22:00:55: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:00:55: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:00:55: #1 total tags in treatment: 10454011 INFO @ Mon, 29 Jun 2020 22:00:55: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:00:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 29 Jun 2020 22:00:55: #1 tags after filtering in treatment: 10454011 INFO @ Mon, 29 Jun 2020 22:00:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:00:55: #1 finished! INFO @ Mon, 29 Jun 2020 22:00:55: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:00:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:00:56: #2 number of paired peaks: 146 WARNING @ Mon, 29 Jun 2020 22:00:56: Fewer paired peaks (146) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 146 pairs to build model! INFO @ Mon, 29 Jun 2020 22:00:56: start model_add_line... INFO @ Mon, 29 Jun 2020 22:00:56: start X-correlation... INFO @ Mon, 29 Jun 2020 22:00:56: end of X-cor INFO @ Mon, 29 Jun 2020 22:00:56: #2 finished! INFO @ Mon, 29 Jun 2020 22:00:56: #2 predicted fragment length is 35 bps INFO @ Mon, 29 Jun 2020 22:00:56: #2 alternative fragment length(s) may be 35 bps INFO @ Mon, 29 Jun 2020 22:00:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.20_model.r WARNING @ Mon, 29 Jun 2020 22:00:56: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:00:56: #2 You may need to consider one of the other alternative d(s): 35 WARNING @ Mon, 29 Jun 2020 22:00:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 29 Jun 2020 22:00:56: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:00:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:01:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:01:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:01:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.10_summits.bed INFO @ Mon, 29 Jun 2020 22:01:02: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (454 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:01:19: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:01:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:01:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:01:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX016169/SRX016169.20_summits.bed INFO @ Mon, 29 Jun 2020 22:01:30: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (349 records, 4 fields): 1 millis CompletedMACS2peakCalling