Job ID = 6527849 SRX = SRX287869 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:27:52 prefetch.2.10.7: 1) Downloading 'SRR870058'... 2020-06-29T13:27:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:31:18 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:31:18 prefetch.2.10.7: 1) 'SRR870058' was downloaded successfully Read 26924228 spots for SRR870058/SRR870058.sra Written 26924228 spots for SRR870058/SRR870058.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: 00:10:50 26924228 reads; of these: 26924228 (100.00%) were unpaired; of these: 1125799 (4.18%) aligned 0 times 17097062 (63.50%) aligned exactly 1 time 8701367 (32.32%) aligned >1 times 95.82% overall alignment rate Time searching: 00:10:50 Overall time: 00:10:50 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] 3992389 / 25798429 = 0.1548 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 22:55:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.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 22:55:32: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:55:32: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:55:38: 1000000 INFO @ Mon, 29 Jun 2020 22:55:44: 2000000 INFO @ Mon, 29 Jun 2020 22:55:50: 3000000 INFO @ Mon, 29 Jun 2020 22:55:56: 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 @ Mon, 29 Jun 2020 22:56:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.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 22:56:02: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:56:02: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:56:02: 5000000 INFO @ Mon, 29 Jun 2020 22:56:08: 1000000 INFO @ Mon, 29 Jun 2020 22:56:09: 6000000 INFO @ Mon, 29 Jun 2020 22:56:15: 2000000 INFO @ Mon, 29 Jun 2020 22:56:15: 7000000 INFO @ Mon, 29 Jun 2020 22:56:21: 3000000 INFO @ Mon, 29 Jun 2020 22:56:22: 8000000 INFO @ Mon, 29 Jun 2020 22:56:28: 4000000 INFO @ Mon, 29 Jun 2020 22:56:28: 9000000 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 22:56:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.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 22:56:32: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:56:32: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:56:35: 5000000 INFO @ Mon, 29 Jun 2020 22:56:35: 10000000 INFO @ Mon, 29 Jun 2020 22:56:40: 1000000 INFO @ Mon, 29 Jun 2020 22:56:42: 6000000 INFO @ Mon, 29 Jun 2020 22:56:42: 11000000 INFO @ Mon, 29 Jun 2020 22:56:47: 2000000 INFO @ Mon, 29 Jun 2020 22:56:49: 7000000 INFO @ Mon, 29 Jun 2020 22:56:49: 12000000 INFO @ Mon, 29 Jun 2020 22:56:55: 3000000 INFO @ Mon, 29 Jun 2020 22:56:55: 8000000 INFO @ Mon, 29 Jun 2020 22:56:56: 13000000 INFO @ Mon, 29 Jun 2020 22:57:02: 9000000 INFO @ Mon, 29 Jun 2020 22:57:02: 4000000 INFO @ Mon, 29 Jun 2020 22:57:03: 14000000 INFO @ Mon, 29 Jun 2020 22:57:09: 10000000 INFO @ Mon, 29 Jun 2020 22:57:10: 15000000 INFO @ Mon, 29 Jun 2020 22:57:10: 5000000 INFO @ Mon, 29 Jun 2020 22:57:16: 11000000 INFO @ Mon, 29 Jun 2020 22:57:17: 16000000 INFO @ Mon, 29 Jun 2020 22:57:18: 6000000 INFO @ Mon, 29 Jun 2020 22:57:23: 12000000 INFO @ Mon, 29 Jun 2020 22:57:23: 17000000 INFO @ Mon, 29 Jun 2020 22:57:25: 7000000 INFO @ Mon, 29 Jun 2020 22:57:29: 13000000 INFO @ Mon, 29 Jun 2020 22:57:30: 18000000 INFO @ Mon, 29 Jun 2020 22:57:33: 8000000 INFO @ Mon, 29 Jun 2020 22:57:36: 14000000 INFO @ Mon, 29 Jun 2020 22:57:38: 19000000 INFO @ Mon, 29 Jun 2020 22:57:40: 9000000 INFO @ Mon, 29 Jun 2020 22:57:43: 15000000 INFO @ Mon, 29 Jun 2020 22:57:44: 20000000 INFO @ Mon, 29 Jun 2020 22:57:48: 10000000 INFO @ Mon, 29 Jun 2020 22:57:50: 16000000 INFO @ Mon, 29 Jun 2020 22:57:51: 21000000 INFO @ Mon, 29 Jun 2020 22:57:55: 11000000 INFO @ Mon, 29 Jun 2020 22:57:57: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:57:57: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:57:57: #1 total tags in treatment: 21806040 INFO @ Mon, 29 Jun 2020 22:57:57: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:57:57: #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 22:57:57: 17000000 INFO @ Mon, 29 Jun 2020 22:57:57: #1 tags after filtering in treatment: 21806040 INFO @ Mon, 29 Jun 2020 22:57:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:57:57: #1 finished! INFO @ Mon, 29 Jun 2020 22:57:57: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:57:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:57:59: #2 number of paired peaks: 166 WARNING @ Mon, 29 Jun 2020 22:57:59: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Mon, 29 Jun 2020 22:57:59: start model_add_line... INFO @ Mon, 29 Jun 2020 22:57:59: start X-correlation... INFO @ Mon, 29 Jun 2020 22:57:59: end of X-cor INFO @ Mon, 29 Jun 2020 22:57:59: #2 finished! INFO @ Mon, 29 Jun 2020 22:57:59: #2 predicted fragment length is 42 bps INFO @ Mon, 29 Jun 2020 22:57:59: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 29 Jun 2020 22:57:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.05_model.r WARNING @ Mon, 29 Jun 2020 22:57:59: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:57:59: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 29 Jun 2020 22:57:59: #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 22:57:59: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:57:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:58:03: 12000000 INFO @ Mon, 29 Jun 2020 22:58:03: 18000000 INFO @ Mon, 29 Jun 2020 22:58:10: 13000000 INFO @ Mon, 29 Jun 2020 22:58:10: 19000000 INFO @ Mon, 29 Jun 2020 22:58:16: 20000000 INFO @ Mon, 29 Jun 2020 22:58:17: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:58:23: 21000000 INFO @ Mon, 29 Jun 2020 22:58:25: 15000000 INFO @ Mon, 29 Jun 2020 22:58:28: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:58:28: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:58:28: #1 total tags in treatment: 21806040 INFO @ Mon, 29 Jun 2020 22:58:28: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:58:28: #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 22:58:29: #1 tags after filtering in treatment: 21806040 INFO @ Mon, 29 Jun 2020 22:58:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:58:29: #1 finished! INFO @ Mon, 29 Jun 2020 22:58:29: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:58:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:58:30: #2 number of paired peaks: 166 WARNING @ Mon, 29 Jun 2020 22:58:30: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Mon, 29 Jun 2020 22:58:30: start model_add_line... INFO @ Mon, 29 Jun 2020 22:58:30: start X-correlation... INFO @ Mon, 29 Jun 2020 22:58:30: end of X-cor INFO @ Mon, 29 Jun 2020 22:58:30: #2 finished! INFO @ Mon, 29 Jun 2020 22:58:30: #2 predicted fragment length is 42 bps INFO @ Mon, 29 Jun 2020 22:58:30: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 29 Jun 2020 22:58:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.10_model.r WARNING @ Mon, 29 Jun 2020 22:58:30: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:58:30: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 29 Jun 2020 22:58:30: #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 22:58:30: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:58:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:58:32: 16000000 INFO @ Mon, 29 Jun 2020 22:58:38: 17000000 INFO @ Mon, 29 Jun 2020 22:58:39: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:58:45: 18000000 INFO @ Mon, 29 Jun 2020 22:58:52: 19000000 INFO @ Mon, 29 Jun 2020 22:58:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:58:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:58:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.05_summits.bed INFO @ Mon, 29 Jun 2020 22:58:58: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2246 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:58:58: 20000000 INFO @ Mon, 29 Jun 2020 22:59:05: 21000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:59:10: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:59:10: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:59:10: #1 total tags in treatment: 21806040 INFO @ Mon, 29 Jun 2020 22:59:10: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:59:10: #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 22:59:10: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:59:11: #1 tags after filtering in treatment: 21806040 INFO @ Mon, 29 Jun 2020 22:59:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:59:11: #1 finished! INFO @ Mon, 29 Jun 2020 22:59:11: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:59:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:59:12: #2 number of paired peaks: 166 WARNING @ Mon, 29 Jun 2020 22:59:12: Fewer paired peaks (166) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 166 pairs to build model! INFO @ Mon, 29 Jun 2020 22:59:12: start model_add_line... INFO @ Mon, 29 Jun 2020 22:59:12: start X-correlation... INFO @ Mon, 29 Jun 2020 22:59:12: end of X-cor INFO @ Mon, 29 Jun 2020 22:59:12: #2 finished! INFO @ Mon, 29 Jun 2020 22:59:12: #2 predicted fragment length is 42 bps INFO @ Mon, 29 Jun 2020 22:59:12: #2 alternative fragment length(s) may be 42 bps INFO @ Mon, 29 Jun 2020 22:59:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.20_model.r WARNING @ Mon, 29 Jun 2020 22:59:12: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:59:12: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Mon, 29 Jun 2020 22:59:12: #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 22:59:12: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:59:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:59:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:59:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:59:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.10_summits.bed INFO @ Mon, 29 Jun 2020 22:59:29: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1889 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:59:52: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:00:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:00:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:00:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287869/SRX287869.20_summits.bed INFO @ Mon, 29 Jun 2020 23:00:11: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1452 records, 4 fields): 3 millis CompletedMACS2peakCalling