Job ID = 6527659 SRX = SRX193327 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:13:48 prefetch.2.10.7: 1) Downloading 'SRR585060'... 2020-06-29T13:13:48 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:21:00 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:21:00 prefetch.2.10.7: 1) 'SRR585060' was downloaded successfully Read 41009766 spots for SRR585060/SRR585060.sra Written 41009766 spots for SRR585060/SRR585060.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: 00:14:45 41009766 reads; of these: 41009766 (100.00%) were unpaired; of these: 1166568 (2.84%) aligned 0 times 25028947 (61.03%) aligned exactly 1 time 14814251 (36.12%) aligned >1 times 97.16% overall alignment rate Time searching: 00:14:45 Overall time: 00:14:45 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 9296103 / 39843198 = 0.2333 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 22:55:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.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 22:55:00: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:55:00: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:55:05: 1000000 INFO @ Mon, 29 Jun 2020 22:55:10: 2000000 INFO @ Mon, 29 Jun 2020 22:55:15: 3000000 INFO @ Mon, 29 Jun 2020 22:55:20: 4000000 INFO @ Mon, 29 Jun 2020 22:55:26: 5000000 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 22:55:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.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 22:55:29: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:55:29: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:55:31: 6000000 INFO @ Mon, 29 Jun 2020 22:55:35: 1000000 INFO @ Mon, 29 Jun 2020 22:55:37: 7000000 INFO @ Mon, 29 Jun 2020 22:55:40: 2000000 INFO @ Mon, 29 Jun 2020 22:55:42: 8000000 INFO @ Mon, 29 Jun 2020 22:55:46: 3000000 INFO @ Mon, 29 Jun 2020 22:55:48: 9000000 INFO @ Mon, 29 Jun 2020 22:55:52: 4000000 INFO @ Mon, 29 Jun 2020 22:55:54: 10000000 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 22:55:58: 5000000 INFO @ Mon, 29 Jun 2020 22:55:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.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 22:55:59: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:55:59: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:56:00: 11000000 INFO @ Mon, 29 Jun 2020 22:56:04: 6000000 INFO @ Mon, 29 Jun 2020 22:56:06: 12000000 INFO @ Mon, 29 Jun 2020 22:56:06: 1000000 INFO @ Mon, 29 Jun 2020 22:56:10: 7000000 INFO @ Mon, 29 Jun 2020 22:56:12: 13000000 INFO @ Mon, 29 Jun 2020 22:56:12: 2000000 INFO @ Mon, 29 Jun 2020 22:56:16: 8000000 INFO @ Mon, 29 Jun 2020 22:56:18: 14000000 INFO @ Mon, 29 Jun 2020 22:56:19: 3000000 INFO @ Mon, 29 Jun 2020 22:56:22: 9000000 INFO @ Mon, 29 Jun 2020 22:56:24: 15000000 INFO @ Mon, 29 Jun 2020 22:56:26: 4000000 INFO @ Mon, 29 Jun 2020 22:56:28: 10000000 INFO @ Mon, 29 Jun 2020 22:56:30: 16000000 INFO @ Mon, 29 Jun 2020 22:56:33: 5000000 INFO @ Mon, 29 Jun 2020 22:56:34: 11000000 INFO @ Mon, 29 Jun 2020 22:56:36: 17000000 INFO @ Mon, 29 Jun 2020 22:56:40: 6000000 INFO @ Mon, 29 Jun 2020 22:56:40: 12000000 INFO @ Mon, 29 Jun 2020 22:56:42: 18000000 INFO @ Mon, 29 Jun 2020 22:56:46: 13000000 INFO @ Mon, 29 Jun 2020 22:56:47: 7000000 INFO @ Mon, 29 Jun 2020 22:56:48: 19000000 INFO @ Mon, 29 Jun 2020 22:56:53: 14000000 INFO @ Mon, 29 Jun 2020 22:56:53: 8000000 INFO @ Mon, 29 Jun 2020 22:56:54: 20000000 INFO @ Mon, 29 Jun 2020 22:56:59: 15000000 INFO @ Mon, 29 Jun 2020 22:57:00: 9000000 INFO @ Mon, 29 Jun 2020 22:57:00: 21000000 INFO @ Mon, 29 Jun 2020 22:57:05: 16000000 INFO @ Mon, 29 Jun 2020 22:57:06: 22000000 INFO @ Mon, 29 Jun 2020 22:57:07: 10000000 INFO @ Mon, 29 Jun 2020 22:57:11: 17000000 INFO @ Mon, 29 Jun 2020 22:57:13: 23000000 INFO @ Mon, 29 Jun 2020 22:57:14: 11000000 INFO @ Mon, 29 Jun 2020 22:57:17: 18000000 INFO @ Mon, 29 Jun 2020 22:57:19: 24000000 INFO @ Mon, 29 Jun 2020 22:57:21: 12000000 INFO @ Mon, 29 Jun 2020 22:57:23: 19000000 INFO @ Mon, 29 Jun 2020 22:57:25: 25000000 INFO @ Mon, 29 Jun 2020 22:57:27: 13000000 INFO @ Mon, 29 Jun 2020 22:57:30: 20000000 INFO @ Mon, 29 Jun 2020 22:57:31: 26000000 INFO @ Mon, 29 Jun 2020 22:57:34: 14000000 INFO @ Mon, 29 Jun 2020 22:57:36: 21000000 INFO @ Mon, 29 Jun 2020 22:57:38: 27000000 INFO @ Mon, 29 Jun 2020 22:57:41: 15000000 INFO @ Mon, 29 Jun 2020 22:57:42: 22000000 INFO @ Mon, 29 Jun 2020 22:57:44: 28000000 INFO @ Mon, 29 Jun 2020 22:57:48: 16000000 INFO @ Mon, 29 Jun 2020 22:57:48: 23000000 INFO @ Mon, 29 Jun 2020 22:57:50: 29000000 INFO @ Mon, 29 Jun 2020 22:57:54: 17000000 INFO @ Mon, 29 Jun 2020 22:57:54: 24000000 INFO @ Mon, 29 Jun 2020 22:57:56: 30000000 INFO @ Mon, 29 Jun 2020 22:58:00: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:58:00: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:58:00: #1 total tags in treatment: 30547095 INFO @ Mon, 29 Jun 2020 22:58:00: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:58:00: #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 22:58:00: #1 tags after filtering in treatment: 30547095 INFO @ Mon, 29 Jun 2020 22:58:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:58:00: #1 finished! INFO @ Mon, 29 Jun 2020 22:58:00: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:58:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:58:01: 25000000 INFO @ Mon, 29 Jun 2020 22:58:01: 18000000 INFO @ Mon, 29 Jun 2020 22:58:02: #2 number of paired peaks: 202 WARNING @ Mon, 29 Jun 2020 22:58:02: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Mon, 29 Jun 2020 22:58:02: start model_add_line... INFO @ Mon, 29 Jun 2020 22:58:02: start X-correlation... INFO @ Mon, 29 Jun 2020 22:58:02: end of X-cor INFO @ Mon, 29 Jun 2020 22:58:02: #2 finished! INFO @ Mon, 29 Jun 2020 22:58:02: #2 predicted fragment length is 51 bps INFO @ Mon, 29 Jun 2020 22:58:02: #2 alternative fragment length(s) may be 1,51,529,576 bps INFO @ Mon, 29 Jun 2020 22:58:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.05_model.r WARNING @ Mon, 29 Jun 2020 22:58:02: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:58:02: #2 You may need to consider one of the other alternative d(s): 1,51,529,576 WARNING @ Mon, 29 Jun 2020 22:58:02: #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 22:58:02: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:58:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:58:07: 26000000 INFO @ Mon, 29 Jun 2020 22:58:08: 19000000 INFO @ Mon, 29 Jun 2020 22:58:13: 27000000 INFO @ Mon, 29 Jun 2020 22:58:14: 20000000 INFO @ Mon, 29 Jun 2020 22:58:19: 28000000 INFO @ Mon, 29 Jun 2020 22:58:21: 21000000 INFO @ Mon, 29 Jun 2020 22:58:25: 29000000 INFO @ Mon, 29 Jun 2020 22:58:28: 22000000 INFO @ Mon, 29 Jun 2020 22:58:32: 30000000 INFO @ Mon, 29 Jun 2020 22:58:35: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:58:35: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:58:35: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:58:35: #1 total tags in treatment: 30547095 INFO @ Mon, 29 Jun 2020 22:58:35: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:58:35: #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 22:58:36: #1 tags after filtering in treatment: 30547095 INFO @ Mon, 29 Jun 2020 22:58:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:58:36: #1 finished! INFO @ Mon, 29 Jun 2020 22:58:36: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:58:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:58:38: #2 number of paired peaks: 202 WARNING @ Mon, 29 Jun 2020 22:58:38: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Mon, 29 Jun 2020 22:58:38: start model_add_line... INFO @ Mon, 29 Jun 2020 22:58:38: start X-correlation... INFO @ Mon, 29 Jun 2020 22:58:38: end of X-cor INFO @ Mon, 29 Jun 2020 22:58:38: #2 finished! INFO @ Mon, 29 Jun 2020 22:58:38: #2 predicted fragment length is 51 bps INFO @ Mon, 29 Jun 2020 22:58:38: #2 alternative fragment length(s) may be 1,51,529,576 bps INFO @ Mon, 29 Jun 2020 22:58:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.10_model.r WARNING @ Mon, 29 Jun 2020 22:58:38: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:58:38: #2 You may need to consider one of the other alternative d(s): 1,51,529,576 WARNING @ Mon, 29 Jun 2020 22:58:38: #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 22:58:38: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:58:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:58:42: 24000000 INFO @ Mon, 29 Jun 2020 22:58:48: 25000000 INFO @ Mon, 29 Jun 2020 22:58:53: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:58:55: 26000000 INFO @ Mon, 29 Jun 2020 22:59:01: 27000000 INFO @ Mon, 29 Jun 2020 22:59:08: 28000000 INFO @ Mon, 29 Jun 2020 22:59:15: 29000000 INFO @ Mon, 29 Jun 2020 22:59:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:59:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:59:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.05_summits.bed INFO @ Mon, 29 Jun 2020 22:59:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4260 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:59:21: 30000000 INFO @ Mon, 29 Jun 2020 22:59:25: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:59:25: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:59:25: #1 total tags in treatment: 30547095 INFO @ Mon, 29 Jun 2020 22:59:25: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:59:25: #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 22:59:25: #1 tags after filtering in treatment: 30547095 INFO @ Mon, 29 Jun 2020 22:59:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:59:25: #1 finished! INFO @ Mon, 29 Jun 2020 22:59:25: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:59:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:59:27: #2 number of paired peaks: 202 WARNING @ Mon, 29 Jun 2020 22:59:27: Fewer paired peaks (202) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 202 pairs to build model! INFO @ Mon, 29 Jun 2020 22:59:27: start model_add_line... INFO @ Mon, 29 Jun 2020 22:59:27: start X-correlation... INFO @ Mon, 29 Jun 2020 22:59:27: end of X-cor INFO @ Mon, 29 Jun 2020 22:59:27: #2 finished! INFO @ Mon, 29 Jun 2020 22:59:27: #2 predicted fragment length is 51 bps INFO @ Mon, 29 Jun 2020 22:59:27: #2 alternative fragment length(s) may be 1,51,529,576 bps INFO @ Mon, 29 Jun 2020 22:59:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.20_model.r WARNING @ Mon, 29 Jun 2020 22:59:27: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:59:27: #2 You may need to consider one of the other alternative d(s): 1,51,529,576 WARNING @ Mon, 29 Jun 2020 22:59:27: #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 22:59:27: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:59:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:59:30: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:59:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:59:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:59:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.10_summits.bed INFO @ Mon, 29 Jun 2020 22:59:55: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2734 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 23:00:19: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 23:00:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.20_peaks.xls INFO @ Mon, 29 Jun 2020 23:00:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 23:00:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX193327/SRX193327.20_summits.bed INFO @ Mon, 29 Jun 2020 23:00:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1244 records, 4 fields): 2 millis CompletedMACS2peakCalling