Job ID = 6627561 SRX = SRX8521400 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-07-14T02:59:37 prefetch.2.10.7: 1) Downloading 'SRR11978342'... 2020-07-14T02:59:37 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:01:05 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:01:05 prefetch.2.10.7: 'SRR11978342' is valid 2020-07-14T03:01:05 prefetch.2.10.7: 1) 'SRR11978342' was downloaded successfully 2020-07-14T03:01:05 prefetch.2.10.7: 'SRR11978342' has 0 unresolved dependencies Read 12258650 spots for SRR11978342/SRR11978342.sra Written 12258650 spots for SRR11978342/SRR11978342.sra 2020-07-14T03:02:22 prefetch.2.10.7: 1) Downloading 'SRR11978343'... 2020-07-14T03:02:22 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:03:53 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:03:54 prefetch.2.10.7: 'SRR11978343' is valid 2020-07-14T03:03:54 prefetch.2.10.7: 1) 'SRR11978343' was downloaded successfully 2020-07-14T03:03:54 prefetch.2.10.7: 'SRR11978343' has 0 unresolved dependencies Read 12210155 spots for SRR11978343/SRR11978343.sra Written 12210155 spots for SRR11978343/SRR11978343.sra 2020-07-14T03:04:49 prefetch.2.10.7: 1) Downloading 'SRR11978344'... 2020-07-14T03:04:49 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:06:19 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:06:19 prefetch.2.10.7: 'SRR11978344' is valid 2020-07-14T03:06:19 prefetch.2.10.7: 1) 'SRR11978344' was downloaded successfully 2020-07-14T03:06:19 prefetch.2.10.7: 'SRR11978344' has 0 unresolved dependencies Read 12471541 spots for SRR11978344/SRR11978344.sra Written 12471541 spots for SRR11978344/SRR11978344.sra 2020-07-14T03:07:17 prefetch.2.10.7: 1) Downloading 'SRR11978345'... 2020-07-14T03:07:17 prefetch.2.10.7: Downloading via HTTPS... 2020-07-14T03:11:25 prefetch.2.10.7: HTTPS download succeed 2020-07-14T03:11:26 prefetch.2.10.7: 'SRR11978345' is valid 2020-07-14T03:11:26 prefetch.2.10.7: 1) 'SRR11978345' was downloaded successfully 2020-07-14T03:11:26 prefetch.2.10.7: 'SRR11978345' has 0 unresolved dependencies Read 12271041 spots for SRR11978345/SRR11978345.sra Written 12271041 spots for SRR11978345/SRR11978345.sra fastq に変換しました。 bowtie でマッピング中... Your job 6627763 ("srTdm6") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:09 49211387 reads; of these: 49211387 (100.00%) were unpaired; of these: 38735742 (78.71%) aligned 0 times 7739364 (15.73%) aligned exactly 1 time 2736281 (5.56%) aligned >1 times 21.29% overall alignment rate Time searching: 00:08:10 Overall time: 00:08:10 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] 1828022 / 10475645 = 0.1745 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 12:23:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.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 12:23:50: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:23:50: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:23:57: 1000000 INFO @ Tue, 14 Jul 2020 12:24:03: 2000000 INFO @ Tue, 14 Jul 2020 12:24:09: 3000000 INFO @ Tue, 14 Jul 2020 12:24:15: 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 12:24:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.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 12:24:20: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:24:20: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:24:21: 5000000 INFO @ Tue, 14 Jul 2020 12:24:27: 1000000 INFO @ Tue, 14 Jul 2020 12:24:28: 6000000 INFO @ Tue, 14 Jul 2020 12:24:34: 2000000 INFO @ Tue, 14 Jul 2020 12:24:34: 7000000 INFO @ Tue, 14 Jul 2020 12:24:41: 3000000 INFO @ Tue, 14 Jul 2020 12:24:41: 8000000 INFO @ Tue, 14 Jul 2020 12:24:45: #1 tag size is determined as 60 bps INFO @ Tue, 14 Jul 2020 12:24:45: #1 tag size = 60 INFO @ Tue, 14 Jul 2020 12:24:45: #1 total tags in treatment: 8647623 INFO @ Tue, 14 Jul 2020 12:24:45: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:24:45: #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 12:24:46: #1 tags after filtering in treatment: 8647623 INFO @ Tue, 14 Jul 2020 12:24:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:24:46: #1 finished! INFO @ Tue, 14 Jul 2020 12:24:46: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:24:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:24:46: #2 number of paired peaks: 236 WARNING @ Tue, 14 Jul 2020 12:24:46: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 14 Jul 2020 12:24:46: start model_add_line... INFO @ Tue, 14 Jul 2020 12:24:46: start X-correlation... INFO @ Tue, 14 Jul 2020 12:24:46: end of X-cor INFO @ Tue, 14 Jul 2020 12:24:46: #2 finished! INFO @ Tue, 14 Jul 2020 12:24:46: #2 predicted fragment length is 46 bps INFO @ Tue, 14 Jul 2020 12:24:46: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 14 Jul 2020 12:24:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.05_model.r WARNING @ Tue, 14 Jul 2020 12:24:46: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:24:46: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 14 Jul 2020 12:24:46: #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 12:24:46: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:24:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:24:47: 4000000 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 12:24:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.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 12:24:50: #1 read tag files... INFO @ Tue, 14 Jul 2020 12:24:50: #1 read treatment tags... INFO @ Tue, 14 Jul 2020 12:24:54: 5000000 INFO @ Tue, 14 Jul 2020 12:24:58: 1000000 INFO @ Tue, 14 Jul 2020 12:25:01: 6000000 INFO @ Tue, 14 Jul 2020 12:25:03: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:25:06: 2000000 INFO @ Tue, 14 Jul 2020 12:25:09: 7000000 INFO @ Tue, 14 Jul 2020 12:25:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.05_peaks.xls INFO @ Tue, 14 Jul 2020 12:25:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.05_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:25:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.05_summits.bed INFO @ Tue, 14 Jul 2020 12:25:12: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2039 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:25:16: 3000000 INFO @ Tue, 14 Jul 2020 12:25:16: 8000000 INFO @ Tue, 14 Jul 2020 12:25:20: #1 tag size is determined as 60 bps INFO @ Tue, 14 Jul 2020 12:25:20: #1 tag size = 60 INFO @ Tue, 14 Jul 2020 12:25:20: #1 total tags in treatment: 8647623 INFO @ Tue, 14 Jul 2020 12:25:20: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:25:20: #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 12:25:20: #1 tags after filtering in treatment: 8647623 INFO @ Tue, 14 Jul 2020 12:25:20: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:25:20: #1 finished! INFO @ Tue, 14 Jul 2020 12:25:20: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:25:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:25:21: #2 number of paired peaks: 236 WARNING @ Tue, 14 Jul 2020 12:25:21: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 14 Jul 2020 12:25:21: start model_add_line... INFO @ Tue, 14 Jul 2020 12:25:21: start X-correlation... INFO @ Tue, 14 Jul 2020 12:25:21: end of X-cor INFO @ Tue, 14 Jul 2020 12:25:21: #2 finished! INFO @ Tue, 14 Jul 2020 12:25:21: #2 predicted fragment length is 46 bps INFO @ Tue, 14 Jul 2020 12:25:21: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 14 Jul 2020 12:25:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.10_model.r WARNING @ Tue, 14 Jul 2020 12:25:21: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:25:21: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 14 Jul 2020 12:25:21: #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 12:25:21: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:25:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:25:25: 4000000 INFO @ Tue, 14 Jul 2020 12:25:33: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 14 Jul 2020 12:25:38: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:25:40: 6000000 INFO @ Tue, 14 Jul 2020 12:25:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.10_peaks.xls INFO @ Tue, 14 Jul 2020 12:25:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.10_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:25:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.10_summits.bed INFO @ Tue, 14 Jul 2020 12:25:47: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (900 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 14 Jul 2020 12:25:47: 7000000 BigWig に変換しました。 INFO @ Tue, 14 Jul 2020 12:25:54: 8000000 INFO @ Tue, 14 Jul 2020 12:25:59: #1 tag size is determined as 60 bps INFO @ Tue, 14 Jul 2020 12:25:59: #1 tag size = 60 INFO @ Tue, 14 Jul 2020 12:25:59: #1 total tags in treatment: 8647623 INFO @ Tue, 14 Jul 2020 12:25:59: #1 user defined the maximum tags... INFO @ Tue, 14 Jul 2020 12:25:59: #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 12:25:59: #1 tags after filtering in treatment: 8647623 INFO @ Tue, 14 Jul 2020 12:25:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 14 Jul 2020 12:25:59: #1 finished! INFO @ Tue, 14 Jul 2020 12:25:59: #2 Build Peak Model... INFO @ Tue, 14 Jul 2020 12:25:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 14 Jul 2020 12:26:00: #2 number of paired peaks: 236 WARNING @ Tue, 14 Jul 2020 12:26:00: Fewer paired peaks (236) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 236 pairs to build model! INFO @ Tue, 14 Jul 2020 12:26:00: start model_add_line... INFO @ Tue, 14 Jul 2020 12:26:00: start X-correlation... INFO @ Tue, 14 Jul 2020 12:26:00: end of X-cor INFO @ Tue, 14 Jul 2020 12:26:00: #2 finished! INFO @ Tue, 14 Jul 2020 12:26:00: #2 predicted fragment length is 46 bps INFO @ Tue, 14 Jul 2020 12:26:00: #2 alternative fragment length(s) may be 46 bps INFO @ Tue, 14 Jul 2020 12:26:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.20_model.r WARNING @ Tue, 14 Jul 2020 12:26:00: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 14 Jul 2020 12:26:00: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Tue, 14 Jul 2020 12:26:00: #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 12:26:00: #3 Call peaks... INFO @ Tue, 14 Jul 2020 12:26:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 14 Jul 2020 12:26:17: #3 Call peaks for each chromosome... INFO @ Tue, 14 Jul 2020 12:26:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.20_peaks.xls INFO @ Tue, 14 Jul 2020 12:26:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.20_peaks.narrowPeak INFO @ Tue, 14 Jul 2020 12:26:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX8521400/SRX8521400.20_summits.bed INFO @ Tue, 14 Jul 2020 12:26:25: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (152 records, 4 fields): 2 millis CompletedMACS2peakCalling