Job ID = 6527642 SRX = SRX1837299 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:20:06 prefetch.2.10.7: 1) Downloading 'SRR3657655'... 2020-06-29T13:20:06 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:23:58 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:23:58 prefetch.2.10.7: 1) 'SRR3657655' was downloaded successfully Read 34731005 spots for SRR3657655/SRR3657655.sra Written 34731005 spots for SRR3657655/SRR3657655.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: 00:17:19 34731005 reads; of these: 34731005 (100.00%) were unpaired; of these: 1070741 (3.08%) aligned 0 times 17781473 (51.20%) aligned exactly 1 time 15878791 (45.72%) aligned >1 times 96.92% overall alignment rate Time searching: 00:17:19 Overall time: 00:17:19 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 16 files... [bam_rmdupse_core] 11437295 / 33660264 = 0.3398 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 22:57:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.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 22:57:29: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:57:29: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:57:35: 1000000 INFO @ Mon, 29 Jun 2020 22:57:41: 2000000 INFO @ Mon, 29 Jun 2020 22:57:48: 3000000 INFO @ Mon, 29 Jun 2020 22:57:54: 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 22:57:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.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 22:57:59: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:57:59: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:58:00: 5000000 INFO @ Mon, 29 Jun 2020 22:58:06: 1000000 INFO @ Mon, 29 Jun 2020 22:58:06: 6000000 INFO @ Mon, 29 Jun 2020 22:58:12: 2000000 INFO @ Mon, 29 Jun 2020 22:58:13: 7000000 INFO @ Mon, 29 Jun 2020 22:58:19: 3000000 INFO @ Mon, 29 Jun 2020 22:58:19: 8000000 INFO @ Mon, 29 Jun 2020 22:58:25: 4000000 INFO @ Mon, 29 Jun 2020 22:58:26: 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 22:58:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.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 22:58:29: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:58:29: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:58:32: 5000000 INFO @ Mon, 29 Jun 2020 22:58:32: 10000000 INFO @ Mon, 29 Jun 2020 22:58:36: 1000000 INFO @ Mon, 29 Jun 2020 22:58:39: 6000000 INFO @ Mon, 29 Jun 2020 22:58:39: 11000000 INFO @ Mon, 29 Jun 2020 22:58:43: 2000000 INFO @ Mon, 29 Jun 2020 22:58:45: 7000000 INFO @ Mon, 29 Jun 2020 22:58:45: 12000000 INFO @ Mon, 29 Jun 2020 22:58:49: 3000000 INFO @ Mon, 29 Jun 2020 22:58:52: 8000000 INFO @ Mon, 29 Jun 2020 22:58:52: 13000000 INFO @ Mon, 29 Jun 2020 22:58:56: 4000000 INFO @ Mon, 29 Jun 2020 22:58:58: 14000000 INFO @ Mon, 29 Jun 2020 22:58:58: 9000000 INFO @ Mon, 29 Jun 2020 22:59:03: 5000000 INFO @ Mon, 29 Jun 2020 22:59:05: 10000000 INFO @ Mon, 29 Jun 2020 22:59:05: 15000000 INFO @ Mon, 29 Jun 2020 22:59:09: 6000000 INFO @ Mon, 29 Jun 2020 22:59:12: 16000000 INFO @ Mon, 29 Jun 2020 22:59:12: 11000000 INFO @ Mon, 29 Jun 2020 22:59:16: 7000000 INFO @ Mon, 29 Jun 2020 22:59:18: 17000000 INFO @ Mon, 29 Jun 2020 22:59:18: 12000000 INFO @ Mon, 29 Jun 2020 22:59:23: 8000000 INFO @ Mon, 29 Jun 2020 22:59:25: 18000000 INFO @ Mon, 29 Jun 2020 22:59:25: 13000000 INFO @ Mon, 29 Jun 2020 22:59:29: 9000000 INFO @ Mon, 29 Jun 2020 22:59:31: 19000000 INFO @ Mon, 29 Jun 2020 22:59:31: 14000000 INFO @ Mon, 29 Jun 2020 22:59:36: 10000000 INFO @ Mon, 29 Jun 2020 22:59:38: 20000000 INFO @ Mon, 29 Jun 2020 22:59:38: 15000000 INFO @ Mon, 29 Jun 2020 22:59:42: 11000000 INFO @ Mon, 29 Jun 2020 22:59:44: 21000000 INFO @ Mon, 29 Jun 2020 22:59:45: 16000000 INFO @ Mon, 29 Jun 2020 22:59:49: 12000000 INFO @ Mon, 29 Jun 2020 22:59:51: 22000000 INFO @ Mon, 29 Jun 2020 22:59:51: 17000000 INFO @ Mon, 29 Jun 2020 22:59:52: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 22:59:52: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 22:59:52: #1 total tags in treatment: 22222969 INFO @ Mon, 29 Jun 2020 22:59:52: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:59:52: #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 22:59:52: #1 tags after filtering in treatment: 22222969 INFO @ Mon, 29 Jun 2020 22:59:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:59:52: #1 finished! INFO @ Mon, 29 Jun 2020 22:59:52: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:59:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:59:54: #2 number of paired peaks: 501 WARNING @ Mon, 29 Jun 2020 22:59:54: Fewer paired peaks (501) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 501 pairs to build model! INFO @ Mon, 29 Jun 2020 22:59:54: start model_add_line... INFO @ Mon, 29 Jun 2020 22:59:54: start X-correlation... INFO @ Mon, 29 Jun 2020 22:59:54: end of X-cor INFO @ Mon, 29 Jun 2020 22:59:54: #2 finished! INFO @ Mon, 29 Jun 2020 22:59:54: #2 predicted fragment length is 60 bps INFO @ Mon, 29 Jun 2020 22:59:54: #2 alternative fragment length(s) may be 2,60 bps INFO @ Mon, 29 Jun 2020 22:59:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.05_model.r WARNING @ Mon, 29 Jun 2020 22:59:54: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:59:54: #2 You may need to consider one of the other alternative d(s): 2,60 WARNING @ Mon, 29 Jun 2020 22:59:54: #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 22:59:54: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:59:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:59:55: 13000000 INFO @ Mon, 29 Jun 2020 22:59:58: 18000000 INFO @ Mon, 29 Jun 2020 23:00:02: 14000000 INFO @ Mon, 29 Jun 2020 23:00:04: 19000000 INFO @ Mon, 29 Jun 2020 23:00:09: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 23:00:11: 20000000 INFO @ Mon, 29 Jun 2020 23:00:15: 16000000 INFO @ Mon, 29 Jun 2020 23:00:17: 21000000 INFO @ Mon, 29 Jun 2020 23:00:21: 17000000 INFO @ Mon, 29 Jun 2020 23:00:23: 22000000 INFO @ Mon, 29 Jun 2020 23:00:25: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 23:00:25: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 23:00:25: #1 total tags in treatment: 22222969 INFO @ Mon, 29 Jun 2020 23:00:25: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:00:25: #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 23:00:25: #1 tags after filtering in treatment: 22222969 INFO @ Mon, 29 Jun 2020 23:00:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:00:25: #1 finished! INFO @ Mon, 29 Jun 2020 23:00:25: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:00:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 23:00:27: #2 number of paired peaks: 501 WARNING @ Mon, 29 Jun 2020 23:00:27: Fewer paired peaks (501) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 501 pairs to build model! INFO @ Mon, 29 Jun 2020 23:00:27: start model_add_line... INFO @ Mon, 29 Jun 2020 23:00:27: start X-correlation... INFO @ Mon, 29 Jun 2020 23:00:27: end of X-cor INFO @ Mon, 29 Jun 2020 23:00:27: #2 finished! INFO @ Mon, 29 Jun 2020 23:00:27: #2 predicted fragment length is 60 bps INFO @ Mon, 29 Jun 2020 23:00:27: #2 alternative fragment length(s) may be 2,60 bps INFO @ Mon, 29 Jun 2020 23:00:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.10_model.r WARNING @ Mon, 29 Jun 2020 23:00:27: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:00:27: #2 You may need to consider one of the other alternative d(s): 2,60 WARNING @ Mon, 29 Jun 2020 23:00:27: #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 23:00:27: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:00:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:00:28: 18000000 INFO @ Mon, 29 Jun 2020 23:00:34: 19000000 INFO @ Mon, 29 Jun 2020 23:00:40: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:00:40: 20000000 INFO @ Mon, 29 Jun 2020 23:00:46: 21000000 INFO @ Mon, 29 Jun 2020 23:00:53: 22000000 INFO @ Mon, 29 Jun 2020 23:00:54: #1 tag size is determined as 51 bps INFO @ Mon, 29 Jun 2020 23:00:54: #1 tag size = 51 INFO @ Mon, 29 Jun 2020 23:00:54: #1 total tags in treatment: 22222969 INFO @ Mon, 29 Jun 2020 23:00:54: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 23:00:54: #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 23:00:54: #1 tags after filtering in treatment: 22222969 INFO @ Mon, 29 Jun 2020 23:00:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 23:00:54: #1 finished! INFO @ Mon, 29 Jun 2020 23:00:54: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 23:00:54: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 23:00:56: #2 number of paired peaks: 501 WARNING @ Mon, 29 Jun 2020 23:00:56: Fewer paired peaks (501) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 501 pairs to build model! INFO @ Mon, 29 Jun 2020 23:00:56: start model_add_line... INFO @ Mon, 29 Jun 2020 23:00:56: start X-correlation... INFO @ Mon, 29 Jun 2020 23:00:56: end of X-cor INFO @ Mon, 29 Jun 2020 23:00:56: #2 finished! INFO @ Mon, 29 Jun 2020 23:00:56: #2 predicted fragment length is 60 bps INFO @ Mon, 29 Jun 2020 23:00:56: #2 alternative fragment length(s) may be 2,60 bps INFO @ Mon, 29 Jun 2020 23:00:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.20_model.r WARNING @ Mon, 29 Jun 2020 23:00:56: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 23:00:56: #2 You may need to consider one of the other alternative d(s): 2,60 WARNING @ Mon, 29 Jun 2020 23:00:56: #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 23:00:56: #3 Call peaks... INFO @ Mon, 29 Jun 2020 23:00:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 23:01:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.05_peaks.xls INFO @ Mon, 29 Jun 2020 23:01:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:01:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.05_summits.bed INFO @ Mon, 29 Jun 2020 23:01:04: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (12750 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:01:11: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:01:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.10_peaks.xls INFO @ Mon, 29 Jun 2020 23:01:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:01:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.10_summits.bed INFO @ Mon, 29 Jun 2020 23:01:33: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4399 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:01:40: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:02:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:02:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:02:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1837299/SRX1837299.20_summits.bed INFO @ Mon, 29 Jun 2020 23:02:03: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1469 records, 4 fields): 3 millis CompletedMACS2peakCalling