Job ID = 6458630 SRX = SRX5343158 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:32:52 prefetch.2.10.7: 1) Downloading 'SRR8540858'... 2020-06-21T12:32:52 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:35:49 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:35:49 prefetch.2.10.7: 1) 'SRR8540858' was downloaded successfully 2020-06-21T12:35:49 prefetch.2.10.7: 'SRR8540858' has 0 unresolved dependencies Read 28775092 spots for SRR8540858/SRR8540858.sra Written 28775092 spots for SRR8540858/SRR8540858.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: 00:00:01 Multiseed full-index search: 00:10:44 28775092 reads; of these: 28775092 (100.00%) were unpaired; of these: 1668346 (5.80%) aligned 0 times 18780663 (65.27%) aligned exactly 1 time 8326083 (28.94%) aligned >1 times 94.20% overall alignment rate Time searching: 00:10:45 Overall time: 00:10:45 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 4393030 / 27106746 = 0.1621 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 @ Sun, 21 Jun 2020 21:56:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.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 @ Sun, 21 Jun 2020 21:56:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:56:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:56:26: 1000000 INFO @ Sun, 21 Jun 2020 21:56:32: 2000000 INFO @ Sun, 21 Jun 2020 21:56:38: 3000000 INFO @ Sun, 21 Jun 2020 21:56:44: 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 @ Sun, 21 Jun 2020 21:56:49: 5000000 INFO @ Sun, 21 Jun 2020 21:56:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.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 @ Sun, 21 Jun 2020 21:56:50: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:56:50: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:56:56: 6000000 INFO @ Sun, 21 Jun 2020 21:56:58: 1000000 INFO @ Sun, 21 Jun 2020 21:57:03: 7000000 INFO @ Sun, 21 Jun 2020 21:57:05: 2000000 INFO @ Sun, 21 Jun 2020 21:57:11: 8000000 INFO @ Sun, 21 Jun 2020 21:57:13: 3000000 BedGraph に変換中... INFO @ Sun, 21 Jun 2020 21:57:18: 9000000 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 @ Sun, 21 Jun 2020 21:57:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.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 @ Sun, 21 Jun 2020 21:57:20: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:57:20: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:57:21: 4000000 INFO @ Sun, 21 Jun 2020 21:57:25: 10000000 INFO @ Sun, 21 Jun 2020 21:57:28: 1000000 INFO @ Sun, 21 Jun 2020 21:57:29: 5000000 INFO @ Sun, 21 Jun 2020 21:57:33: 11000000 INFO @ Sun, 21 Jun 2020 21:57:36: 2000000 INFO @ Sun, 21 Jun 2020 21:57:37: 6000000 INFO @ Sun, 21 Jun 2020 21:57:40: 12000000 INFO @ Sun, 21 Jun 2020 21:57:45: 3000000 INFO @ Sun, 21 Jun 2020 21:57:45: 7000000 INFO @ Sun, 21 Jun 2020 21:57:47: 13000000 INFO @ Sun, 21 Jun 2020 21:57:53: 4000000 INFO @ Sun, 21 Jun 2020 21:57:53: 8000000 INFO @ Sun, 21 Jun 2020 21:57:55: 14000000 INFO @ Sun, 21 Jun 2020 21:58:01: 5000000 INFO @ Sun, 21 Jun 2020 21:58:01: 9000000 INFO @ Sun, 21 Jun 2020 21:58:02: 15000000 INFO @ Sun, 21 Jun 2020 21:58:09: 6000000 INFO @ Sun, 21 Jun 2020 21:58:09: 16000000 INFO @ Sun, 21 Jun 2020 21:58:10: 10000000 INFO @ Sun, 21 Jun 2020 21:58:17: 17000000 INFO @ Sun, 21 Jun 2020 21:58:18: 7000000 INFO @ Sun, 21 Jun 2020 21:58:18: 11000000 INFO @ Sun, 21 Jun 2020 21:58:24: 18000000 INFO @ Sun, 21 Jun 2020 21:58:26: 8000000 INFO @ Sun, 21 Jun 2020 21:58:26: 12000000 INFO @ Sun, 21 Jun 2020 21:58:32: 19000000 INFO @ Sun, 21 Jun 2020 21:58:34: 9000000 INFO @ Sun, 21 Jun 2020 21:58:35: 13000000 INFO @ Sun, 21 Jun 2020 21:58:39: 20000000 INFO @ Sun, 21 Jun 2020 21:58:42: 10000000 INFO @ Sun, 21 Jun 2020 21:58:43: 14000000 INFO @ Sun, 21 Jun 2020 21:58:47: 21000000 INFO @ Sun, 21 Jun 2020 21:58:50: 11000000 INFO @ Sun, 21 Jun 2020 21:58:51: 15000000 INFO @ Sun, 21 Jun 2020 21:58:54: 22000000 INFO @ Sun, 21 Jun 2020 21:58:58: 12000000 INFO @ Sun, 21 Jun 2020 21:58:59: 16000000 INFO @ Sun, 21 Jun 2020 21:59:00: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:59:00: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:59:00: #1 total tags in treatment: 22713716 INFO @ Sun, 21 Jun 2020 21:59:00: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:59:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:59:00: #1 tags after filtering in treatment: 22713714 INFO @ Sun, 21 Jun 2020 21:59:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:59:00: #1 finished! INFO @ Sun, 21 Jun 2020 21:59:00: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:59:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:59:02: #2 number of paired peaks: 218 WARNING @ Sun, 21 Jun 2020 21:59:02: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Sun, 21 Jun 2020 21:59:02: start model_add_line... INFO @ Sun, 21 Jun 2020 21:59:02: start X-correlation... INFO @ Sun, 21 Jun 2020 21:59:02: end of X-cor INFO @ Sun, 21 Jun 2020 21:59:02: #2 finished! INFO @ Sun, 21 Jun 2020 21:59:02: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 21:59:02: #2 alternative fragment length(s) may be 2,43 bps INFO @ Sun, 21 Jun 2020 21:59:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.05_model.r WARNING @ Sun, 21 Jun 2020 21:59:02: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:59:02: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Sun, 21 Jun 2020 21:59:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:59:02: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:59:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:59:06: 13000000 INFO @ Sun, 21 Jun 2020 21:59:07: 17000000 INFO @ Sun, 21 Jun 2020 21:59:15: 14000000 INFO @ Sun, 21 Jun 2020 21:59:15: 18000000 INFO @ Sun, 21 Jun 2020 21:59:23: 15000000 INFO @ Sun, 21 Jun 2020 21:59:24: 19000000 INFO @ Sun, 21 Jun 2020 21:59:31: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:59:32: 20000000 INFO @ Sun, 21 Jun 2020 21:59:39: 17000000 INFO @ Sun, 21 Jun 2020 21:59:40: 21000000 INFO @ Sun, 21 Jun 2020 21:59:44: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:59:47: 18000000 INFO @ Sun, 21 Jun 2020 21:59:49: 22000000 INFO @ Sun, 21 Jun 2020 21:59:55: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 21:59:55: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 21:59:55: #1 total tags in treatment: 22713716 INFO @ Sun, 21 Jun 2020 21:59:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:59:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 21:59:55: 19000000 INFO @ Sun, 21 Jun 2020 21:59:55: #1 tags after filtering in treatment: 22713714 INFO @ Sun, 21 Jun 2020 21:59:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:59:55: #1 finished! INFO @ Sun, 21 Jun 2020 21:59:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:59:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:59:57: #2 number of paired peaks: 218 WARNING @ Sun, 21 Jun 2020 21:59:57: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Sun, 21 Jun 2020 21:59:57: start model_add_line... INFO @ Sun, 21 Jun 2020 21:59:57: start X-correlation... INFO @ Sun, 21 Jun 2020 21:59:57: end of X-cor INFO @ Sun, 21 Jun 2020 21:59:57: #2 finished! INFO @ Sun, 21 Jun 2020 21:59:57: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 21:59:57: #2 alternative fragment length(s) may be 2,43 bps INFO @ Sun, 21 Jun 2020 21:59:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.10_model.r WARNING @ Sun, 21 Jun 2020 21:59:57: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:59:57: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Sun, 21 Jun 2020 21:59:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 21:59:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:59:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 22:00:03: 20000000 INFO @ Sun, 21 Jun 2020 22:00:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.05_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.05_summits.bed INFO @ Sun, 21 Jun 2020 22:00:05: Done! pass1 - making usageList (700 chroms): 2 millis pass2 - checking and writing primary data (2512 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:00:10: 21000000 INFO @ Sun, 21 Jun 2020 22:00:18: 22000000 INFO @ Sun, 21 Jun 2020 22:00:23: #1 tag size is determined as 65 bps INFO @ Sun, 21 Jun 2020 22:00:23: #1 tag size = 65 INFO @ Sun, 21 Jun 2020 22:00:23: #1 total tags in treatment: 22713716 INFO @ Sun, 21 Jun 2020 22:00:23: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 22:00:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 22:00:24: #1 tags after filtering in treatment: 22713714 INFO @ Sun, 21 Jun 2020 22:00:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 22:00:24: #1 finished! INFO @ Sun, 21 Jun 2020 22:00:24: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 22:00:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 22:00:25: #2 number of paired peaks: 218 WARNING @ Sun, 21 Jun 2020 22:00:25: Fewer paired peaks (218) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 218 pairs to build model! INFO @ Sun, 21 Jun 2020 22:00:25: start model_add_line... INFO @ Sun, 21 Jun 2020 22:00:26: start X-correlation... INFO @ Sun, 21 Jun 2020 22:00:26: end of X-cor INFO @ Sun, 21 Jun 2020 22:00:26: #2 finished! INFO @ Sun, 21 Jun 2020 22:00:26: #2 predicted fragment length is 43 bps INFO @ Sun, 21 Jun 2020 22:00:26: #2 alternative fragment length(s) may be 2,43 bps INFO @ Sun, 21 Jun 2020 22:00:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.20_model.r WARNING @ Sun, 21 Jun 2020 22:00:26: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 22:00:26: #2 You may need to consider one of the other alternative d(s): 2,43 WARNING @ Sun, 21 Jun 2020 22:00:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 22:00:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 22:00:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 22:00:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:00:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.10_peaks.xls INFO @ Sun, 21 Jun 2020 22:00:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:00:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.10_summits.bed INFO @ Sun, 21 Jun 2020 22:00:59: Done! pass1 - making usageList (553 chroms): 1 millis pass2 - checking and writing primary data (1643 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 22:01:07: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 22:01:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.20_peaks.xls INFO @ Sun, 21 Jun 2020 22:01:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 22:01:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5343158/SRX5343158.20_summits.bed INFO @ Sun, 21 Jun 2020 22:01:28: Done! pass1 - making usageList (261 chroms): 1 millis pass2 - checking and writing primary data (523 records, 4 fields): 9 millis CompletedMACS2peakCalling