Job ID = 6627172 SRX = SRX8521305 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T01:26:19 prefetch.2.10.7: 1) Downloading 'SRR11978669'... 2020-07-14T01:26:19 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:27:38 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:27:38 prefetch.2.10.7: 'SRR11978669' is valid 2020-07-14T01:27:38 prefetch.2.10.7: 1) 'SRR11978669' was downloaded successfully 2020-07-14T01:27:38 prefetch.2.10.7: 'SRR11978669' has 0 unresolved dependencies Read 11264107 spots for SRR11978669/SRR11978669.sra Written 11264107 spots for SRR11978669/SRR11978669.sra 2020-07-14T01:28:26 prefetch.2.10.7: 1) Downloading 'SRR11978670'... 2020-07-14T01:28:26 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:30:07 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:30:07 prefetch.2.10.7: 'SRR11978670' is valid 2020-07-14T01:30:07 prefetch.2.10.7: 1) 'SRR11978670' was downloaded successfully 2020-07-14T01:30:07 prefetch.2.10.7: 'SRR11978670' has 0 unresolved dependencies Read 11125320 spots for SRR11978670/SRR11978670.sra Written 11125320 spots for SRR11978670/SRR11978670.sra 2020-07-14T01:30:58 prefetch.2.10.7: 1) Downloading 'SRR11978671'... 2020-07-14T01:30:58 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:31:58 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:31:59 prefetch.2.10.7: 'SRR11978671' is valid 2020-07-14T01:31:59 prefetch.2.10.7: 1) 'SRR11978671' was downloaded successfully 2020-07-14T01:31:59 prefetch.2.10.7: 'SRR11978671' has 0 unresolved dependencies Read 11438598 spots for SRR11978671/SRR11978671.sra Written 11438598 spots for SRR11978671/SRR11978671.sra 2020-07-14T01:32:46 prefetch.2.10.7: 1) Downloading 'SRR11978672'... 2020-07-14T01:32:46 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T01:34:10 prefetch.2.10.7: HTTPS download succeed 2020-07-14T01:34:10 prefetch.2.10.7: 'SRR11978672' is valid 2020-07-14T01:34:10 prefetch.2.10.7: 1) 'SRR11978672' was downloaded successfully 2020-07-14T01:34:10 prefetch.2.10.7: 'SRR11978672' has 0 unresolved dependencies Read 11297049 spots for SRR11978672/SRR11978672.sra Written 11297049 spots for SRR11978672/SRR11978672.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627426 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:23 45125074 reads; of these: 45125074 (100.00%) were unpaired; of these: 37182889 (82.40%) aligned 0 times 5812326 (12.88%) aligned exactly 1 time 2129859 (4.72%) aligned >1 times 17.60% overall alignment rate Time searching: 00:07:23 Overall time: 00:07:23 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] 1472708 / 7942185 = 0.1854 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 @ Tue, 14 Jul 2020 10:45:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.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 @ Tue, 14 Jul 2020 10:45:03: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:45:03: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:45:09: 1000000 INFO @ Tue, 14 Jul 2020 10:45:15: 2000000 INFO @ Tue, 14 Jul 2020 10:45:21: 3000000 INFO @ Tue, 14 Jul 2020 10:45:27: 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 @ Tue, 14 Jul 2020 10:45:32: 5000000 INFO @ Tue, 14 Jul 2020 10:45:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.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 @ Tue, 14 Jul 2020 10:45:33: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:45:33: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:45:39: 6000000 INFO @ Tue, 14 Jul 2020 10:45:41: 1000000 INFO @ Tue, 14 Jul 2020 10:45:42: #1 tag size is determined as 65 bps INFO @ Tue, 14 Jul 2020 10:45:42: #1 tag size = 65 INFO @ Tue, 14 Jul 2020 10:45:42: #1 total tags in treatment: 6469477 INFO @ Tue, 14 Jul 2020 10:45:42: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:45:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:45:43: #1 tags after filtering in treatment: 6469477 INFO @ Tue, 14 Jul 2020 10:45:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:45:43: #1 finished! INFO @ Tue, 14 Jul 2020 10:45:43: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:45:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:45:43: #2 number of paired peaks: 316 WARNING @ Tue, 14 Jul 2020 10:45:43: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Tue, 14 Jul 2020 10:45:43: start model_add_line... INFO @ Tue, 14 Jul 2020 10:45:43: start X-correlation... INFO @ Tue, 14 Jul 2020 10:45:43: end of X-cor INFO @ Tue, 14 Jul 2020 10:45:43: #2 finished! INFO @ Tue, 14 Jul 2020 10:45:43: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 10:45:43: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 10:45:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.05_model.r WARNING @ Tue, 14 Jul 2020 10:45:43: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:45:43: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 10:45:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:45:43: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:45:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:45:48: 2000000 INFO @ Tue, 14 Jul 2020 10:45:56: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:45:56: 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 @ Tue, 14 Jul 2020 10:46:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.05_peaks.xls INFO @ Tue, 14 Jul 2020 10:46:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:46:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.05_summits.bed INFO @ Tue, 14 Jul 2020 10:46:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2090 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:46:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.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 @ Tue, 14 Jul 2020 10:46:03: #1 read tag files... INFO @ Tue, 14 Jul 2020 10:46:03: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 10:46:03: 4000000 INFO @ Tue, 14 Jul 2020 10:46:10: 1000000 INFO @ Tue, 14 Jul 2020 10:46:11: 5000000 INFO @ Tue, 14 Jul 2020 10:46:17: 2000000 INFO @ Tue, 14 Jul 2020 10:46:18: 6000000 INFO @ Tue, 14 Jul 2020 10:46:22: #1 tag size is determined as 65 bps INFO @ Tue, 14 Jul 2020 10:46:22: #1 tag size = 65 INFO @ Tue, 14 Jul 2020 10:46:22: #1 total tags in treatment: 6469477 INFO @ Tue, 14 Jul 2020 10:46:22: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:46:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:46:22: #1 tags after filtering in treatment: 6469477 INFO @ Tue, 14 Jul 2020 10:46:22: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:46:22: #1 finished! INFO @ Tue, 14 Jul 2020 10:46:22: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:46:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:46:22: #2 number of paired peaks: 316 WARNING @ Tue, 14 Jul 2020 10:46:22: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Tue, 14 Jul 2020 10:46:22: start model_add_line... INFO @ Tue, 14 Jul 2020 10:46:22: start X-correlation... INFO @ Tue, 14 Jul 2020 10:46:22: end of X-cor INFO @ Tue, 14 Jul 2020 10:46:22: #2 finished! INFO @ Tue, 14 Jul 2020 10:46:22: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 10:46:22: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 10:46:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.10_model.r WARNING @ Tue, 14 Jul 2020 10:46:22: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:46:22: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 10:46:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:46:22: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:46:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 10:46:23: 3000000 INFO @ Tue, 14 Jul 2020 10:46:30: 4000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 10:46:36: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:46:36: 5000000 INFO @ Tue, 14 Jul 2020 10:46:43: 6000000 INFO @ Tue, 14 Jul 2020 10:46:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.10_peaks.xls INFO @ Tue, 14 Jul 2020 10:46:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:46:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.10_summits.bed INFO @ Tue, 14 Jul 2020 10:46:43: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (867 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 10:46:46: #1 tag size is determined as 65 bps INFO @ Tue, 14 Jul 2020 10:46:46: #1 tag size = 65 INFO @ Tue, 14 Jul 2020 10:46:46: #1 total tags in treatment: 6469477 INFO @ Tue, 14 Jul 2020 10:46:46: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 10:46:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 14 Jul 2020 10:46:46: #1 tags after filtering in treatment: 6469477 INFO @ Tue, 14 Jul 2020 10:46:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 10:46:46: #1 finished! INFO @ Tue, 14 Jul 2020 10:46:46: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 10:46:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 10:46:46: #2 number of paired peaks: 316 WARNING @ Tue, 14 Jul 2020 10:46:46: Fewer paired peaks (316) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 316 pairs to build model! INFO @ Tue, 14 Jul 2020 10:46:46: start model_add_line... INFO @ Tue, 14 Jul 2020 10:46:46: start X-correlation... INFO @ Tue, 14 Jul 2020 10:46:46: end of X-cor INFO @ Tue, 14 Jul 2020 10:46:46: #2 finished! INFO @ Tue, 14 Jul 2020 10:46:46: #2 predicted fragment length is 58 bps INFO @ Tue, 14 Jul 2020 10:46:46: #2 alternative fragment length(s) may be 58 bps INFO @ Tue, 14 Jul 2020 10:46:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.20_model.r WARNING @ Tue, 14 Jul 2020 10:46:46: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 10:46:46: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Tue, 14 Jul 2020 10:46:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 14 Jul 2020 10:46:46: #3 Call peaks... INFO @ Tue, 14 Jul 2020 10:46:46: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 10:46:59: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 10:47:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.20_peaks.xls INFO @ Tue, 14 Jul 2020 10:47:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 10:47:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521305/SRX8521305.20_summits.bed INFO @ Tue, 14 Jul 2020 10:47:05: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (194 records, 4 fields): 3 millis CompletedMACS2peakCalling