Job ID = 6452709 SRX = SRX026861 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T08:03:38 prefetch.2.10.7: 1) Downloading 'SRR065760'... 2020-06-21T08:03:38 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:05:38 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:05:39 prefetch.2.10.7: 'SRR065760' is valid 2020-06-21T08:05:39 prefetch.2.10.7: 1) 'SRR065760' was downloaded successfully Read 21236027 spots for SRR065760/SRR065760.sra Written 21236027 spots for SRR065760/SRR065760.sra 2020-06-21T08:06:47 prefetch.2.10.7: 1) Downloading 'SRR065761'... 2020-06-21T08:06:47 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T08:08:51 prefetch.2.10.7: HTTPS download succeed 2020-06-21T08:08:52 prefetch.2.10.7: 'SRR065761' is valid 2020-06-21T08:08:52 prefetch.2.10.7: 1) 'SRR065761' was downloaded successfully Read 22197905 spots for SRR065761/SRR065761.sra Written 22197905 spots for SRR065761/SRR065761.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: 00:14:06 43433932 reads; of these: 43433932 (100.00%) were unpaired; of these: 2281892 (5.25%) aligned 0 times 22129836 (50.95%) aligned exactly 1 time 19022204 (43.80%) aligned >1 times 94.75% overall alignment rate Time searching: 00:14:06 Overall time: 00:14:06 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] 24716606 / 41152040 = 0.6006 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 17:31:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.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 17:31:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:31:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:31:49: 1000000 INFO @ Sun, 21 Jun 2020 17:31:54: 2000000 INFO @ Sun, 21 Jun 2020 17:31:59: 3000000 INFO @ Sun, 21 Jun 2020 17:32:04: 4000000 INFO @ Sun, 21 Jun 2020 17:32:08: 5000000 INFO @ Sun, 21 Jun 2020 17:32:13: 6000000 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 17:32:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.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 17:32:15: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:32:15: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:32:17: 7000000 INFO @ Sun, 21 Jun 2020 17:32:19: 1000000 INFO @ Sun, 21 Jun 2020 17:32:22: 8000000 INFO @ Sun, 21 Jun 2020 17:32:24: 2000000 INFO @ Sun, 21 Jun 2020 17:32:27: 9000000 INFO @ Sun, 21 Jun 2020 17:32:29: 3000000 INFO @ Sun, 21 Jun 2020 17:32:31: 10000000 INFO @ Sun, 21 Jun 2020 17:32:33: 4000000 INFO @ Sun, 21 Jun 2020 17:32:36: 11000000 INFO @ Sun, 21 Jun 2020 17:32:38: 5000000 INFO @ Sun, 21 Jun 2020 17:32:41: 12000000 BedGraph に変換中... INFO @ Sun, 21 Jun 2020 17:32:43: 6000000 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 17:32:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.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 17:32:45: #1 read tag files... INFO @ Sun, 21 Jun 2020 17:32:45: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 17:32:46: 13000000 INFO @ Sun, 21 Jun 2020 17:32:48: 7000000 INFO @ Sun, 21 Jun 2020 17:32:49: 1000000 INFO @ Sun, 21 Jun 2020 17:32:51: 14000000 INFO @ Sun, 21 Jun 2020 17:32:52: 8000000 INFO @ Sun, 21 Jun 2020 17:32:54: 2000000 INFO @ Sun, 21 Jun 2020 17:32:56: 15000000 INFO @ Sun, 21 Jun 2020 17:32:57: 9000000 INFO @ Sun, 21 Jun 2020 17:32:59: 3000000 INFO @ Sun, 21 Jun 2020 17:33:00: 16000000 INFO @ Sun, 21 Jun 2020 17:33:02: 10000000 INFO @ Sun, 21 Jun 2020 17:33:03: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:33:03: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:33:03: #1 total tags in treatment: 16435434 INFO @ Sun, 21 Jun 2020 17:33:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:33:03: #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 17:33:03: #1 tags after filtering in treatment: 16435434 INFO @ Sun, 21 Jun 2020 17:33:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:33:03: #1 finished! INFO @ Sun, 21 Jun 2020 17:33:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:33:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:33:04: 4000000 INFO @ Sun, 21 Jun 2020 17:33:04: #2 number of paired peaks: 1347 INFO @ Sun, 21 Jun 2020 17:33:04: start model_add_line... INFO @ Sun, 21 Jun 2020 17:33:04: start X-correlation... INFO @ Sun, 21 Jun 2020 17:33:05: end of X-cor INFO @ Sun, 21 Jun 2020 17:33:05: #2 finished! INFO @ Sun, 21 Jun 2020 17:33:05: #2 predicted fragment length is 32 bps INFO @ Sun, 21 Jun 2020 17:33:05: #2 alternative fragment length(s) may be 2,32 bps INFO @ Sun, 21 Jun 2020 17:33:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.05_model.r WARNING @ Sun, 21 Jun 2020 17:33:05: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:33:05: #2 You may need to consider one of the other alternative d(s): 2,32 WARNING @ Sun, 21 Jun 2020 17:33:05: #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 17:33:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:33:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:33:07: 11000000 INFO @ Sun, 21 Jun 2020 17:33:08: 5000000 INFO @ Sun, 21 Jun 2020 17:33:11: 12000000 INFO @ Sun, 21 Jun 2020 17:33:13: 6000000 INFO @ Sun, 21 Jun 2020 17:33:17: 13000000 INFO @ Sun, 21 Jun 2020 17:33:18: 7000000 INFO @ Sun, 21 Jun 2020 17:33:21: 14000000 INFO @ Sun, 21 Jun 2020 17:33:23: 8000000 INFO @ Sun, 21 Jun 2020 17:33:26: 15000000 INFO @ Sun, 21 Jun 2020 17:33:27: 9000000 INFO @ Sun, 21 Jun 2020 17:33:31: 16000000 INFO @ Sun, 21 Jun 2020 17:33:32: 10000000 INFO @ Sun, 21 Jun 2020 17:33:33: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:33:33: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:33:33: #1 total tags in treatment: 16435434 INFO @ Sun, 21 Jun 2020 17:33:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:33:33: #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 17:33:34: #1 tags after filtering in treatment: 16435434 INFO @ Sun, 21 Jun 2020 17:33:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:33:34: #1 finished! INFO @ Sun, 21 Jun 2020 17:33:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:33:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:33:35: #2 number of paired peaks: 1347 INFO @ Sun, 21 Jun 2020 17:33:35: start model_add_line... INFO @ Sun, 21 Jun 2020 17:33:35: start X-correlation... INFO @ Sun, 21 Jun 2020 17:33:35: end of X-cor INFO @ Sun, 21 Jun 2020 17:33:35: #2 finished! INFO @ Sun, 21 Jun 2020 17:33:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:33:35: #2 predicted fragment length is 32 bps INFO @ Sun, 21 Jun 2020 17:33:35: #2 alternative fragment length(s) may be 2,32 bps INFO @ Sun, 21 Jun 2020 17:33:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.10_model.r WARNING @ Sun, 21 Jun 2020 17:33:35: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:33:35: #2 You may need to consider one of the other alternative d(s): 2,32 WARNING @ Sun, 21 Jun 2020 17:33:35: #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 17:33:35: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:33:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:33:37: 11000000 INFO @ Sun, 21 Jun 2020 17:33:42: 12000000 INFO @ Sun, 21 Jun 2020 17:33:47: 13000000 INFO @ Sun, 21 Jun 2020 17:33:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.05_peaks.xls INFO @ Sun, 21 Jun 2020 17:33:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:33:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.05_summits.bed INFO @ Sun, 21 Jun 2020 17:33:50: Done! pass1 - making usageList (708 chroms): 2 millis pass2 - checking and writing primary data (3203 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 17:33:51: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 17:33:56: 15000000 INFO @ Sun, 21 Jun 2020 17:34:01: 16000000 INFO @ Sun, 21 Jun 2020 17:34:03: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 17:34:03: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 17:34:03: #1 total tags in treatment: 16435434 INFO @ Sun, 21 Jun 2020 17:34:03: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 17:34:03: #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 17:34:03: #1 tags after filtering in treatment: 16435434 INFO @ Sun, 21 Jun 2020 17:34:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 17:34:03: #1 finished! INFO @ Sun, 21 Jun 2020 17:34:03: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 17:34:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 17:34:05: #2 number of paired peaks: 1347 INFO @ Sun, 21 Jun 2020 17:34:05: start model_add_line... INFO @ Sun, 21 Jun 2020 17:34:05: start X-correlation... INFO @ Sun, 21 Jun 2020 17:34:05: end of X-cor INFO @ Sun, 21 Jun 2020 17:34:05: #2 finished! INFO @ Sun, 21 Jun 2020 17:34:05: #2 predicted fragment length is 32 bps INFO @ Sun, 21 Jun 2020 17:34:05: #2 alternative fragment length(s) may be 2,32 bps INFO @ Sun, 21 Jun 2020 17:34:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.20_model.r WARNING @ Sun, 21 Jun 2020 17:34:05: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 17:34:05: #2 You may need to consider one of the other alternative d(s): 2,32 WARNING @ Sun, 21 Jun 2020 17:34:05: #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 17:34:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 17:34:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 17:34:06: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:34:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.10_peaks.xls INFO @ Sun, 21 Jun 2020 17:34:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:34:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.10_summits.bed INFO @ Sun, 21 Jun 2020 17:34:20: Done! pass1 - making usageList (564 chroms): 2 millis pass2 - checking and writing primary data (2165 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 17:34:35: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 17:34:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.20_peaks.xls INFO @ Sun, 21 Jun 2020 17:34:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 17:34:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX026861/SRX026861.20_summits.bed INFO @ Sun, 21 Jun 2020 17:34:50: Done! pass1 - making usageList (430 chroms): 1 millis pass2 - checking and writing primary data (1803 records, 4 fields): 14 millis CompletedMACS2peakCalling