Job ID = 6454772 SRX = SRX2583185 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:24:14 prefetch.2.10.7: 1) Downloading 'SRR5279385'... 2020-06-21T09:24:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:28:58 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:28:59 prefetch.2.10.7: 'SRR5279385' is valid 2020-06-21T09:28:59 prefetch.2.10.7: 1) 'SRR5279385' was downloaded successfully 2020-06-21T09:28:59 prefetch.2.10.7: 'SRR5279385' has 0 unresolved dependencies Read 22211482 spots for SRR5279385/SRR5279385.sra Written 22211482 spots for SRR5279385/SRR5279385.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:06:34 22211482 reads; of these: 22211482 (100.00%) were unpaired; of these: 657140 (2.96%) aligned 0 times 15577717 (70.13%) aligned exactly 1 time 5976625 (26.91%) aligned >1 times 97.04% overall alignment rate Time searching: 00:06:35 Overall time: 00:06:35 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] 3428593 / 21554342 = 0.1591 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 18:43:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.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 18:43:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:27: 1000000 INFO @ Sun, 21 Jun 2020 18:43:33: 2000000 INFO @ Sun, 21 Jun 2020 18:43:38: 3000000 INFO @ Sun, 21 Jun 2020 18:43:43: 4000000 INFO @ Sun, 21 Jun 2020 18:43:49: 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 @ Sun, 21 Jun 2020 18:43:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.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 18:43:52: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:43:52: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:43:54: 6000000 INFO @ Sun, 21 Jun 2020 18:43:57: 1000000 INFO @ Sun, 21 Jun 2020 18:43:59: 7000000 INFO @ Sun, 21 Jun 2020 18:44:02: 2000000 INFO @ Sun, 21 Jun 2020 18:44:05: 8000000 INFO @ Sun, 21 Jun 2020 18:44:07: 3000000 INFO @ Sun, 21 Jun 2020 18:44:10: 9000000 INFO @ Sun, 21 Jun 2020 18:44:12: 4000000 INFO @ Sun, 21 Jun 2020 18:44:16: 10000000 INFO @ Sun, 21 Jun 2020 18:44:17: 5000000 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 @ Sun, 21 Jun 2020 18:44:21: 11000000 INFO @ Sun, 21 Jun 2020 18:44:22: 6000000 INFO @ Sun, 21 Jun 2020 18:44:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.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 18:44:22: #1 read tag files... INFO @ Sun, 21 Jun 2020 18:44:22: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 18:44:27: 7000000 INFO @ Sun, 21 Jun 2020 18:44:27: 12000000 INFO @ Sun, 21 Jun 2020 18:44:27: 1000000 INFO @ Sun, 21 Jun 2020 18:44:32: 8000000 INFO @ Sun, 21 Jun 2020 18:44:32: 13000000 INFO @ Sun, 21 Jun 2020 18:44:32: 2000000 INFO @ Sun, 21 Jun 2020 18:44:37: 9000000 INFO @ Sun, 21 Jun 2020 18:44:37: 3000000 INFO @ Sun, 21 Jun 2020 18:44:38: 14000000 INFO @ Sun, 21 Jun 2020 18:44:42: 10000000 INFO @ Sun, 21 Jun 2020 18:44:42: 4000000 INFO @ Sun, 21 Jun 2020 18:44:43: 15000000 INFO @ Sun, 21 Jun 2020 18:44:47: 11000000 INFO @ Sun, 21 Jun 2020 18:44:47: 5000000 INFO @ Sun, 21 Jun 2020 18:44:49: 16000000 INFO @ Sun, 21 Jun 2020 18:44:52: 12000000 INFO @ Sun, 21 Jun 2020 18:44:52: 6000000 INFO @ Sun, 21 Jun 2020 18:44:54: 17000000 INFO @ Sun, 21 Jun 2020 18:44:57: 13000000 INFO @ Sun, 21 Jun 2020 18:44:57: 7000000 INFO @ Sun, 21 Jun 2020 18:45:00: 18000000 INFO @ Sun, 21 Jun 2020 18:45:01: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:45:01: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:45:01: #1 total tags in treatment: 18125749 INFO @ Sun, 21 Jun 2020 18:45:01: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:01: #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 18:45:01: #1 tags after filtering in treatment: 18125664 INFO @ Sun, 21 Jun 2020 18:45:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:45:01: #1 finished! INFO @ Sun, 21 Jun 2020 18:45:01: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:45:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:02: 14000000 INFO @ Sun, 21 Jun 2020 18:45:03: 8000000 INFO @ Sun, 21 Jun 2020 18:45:03: #2 number of paired peaks: 570 WARNING @ Sun, 21 Jun 2020 18:45:03: Fewer paired peaks (570) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 570 pairs to build model! INFO @ Sun, 21 Jun 2020 18:45:03: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:03: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:03: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:03: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:03: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 18:45:03: #2 alternative fragment length(s) may be 3,50,587 bps INFO @ Sun, 21 Jun 2020 18:45:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.05_model.r WARNING @ Sun, 21 Jun 2020 18:45:03: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:45:03: #2 You may need to consider one of the other alternative d(s): 3,50,587 WARNING @ Sun, 21 Jun 2020 18:45:03: #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 18:45:03: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:45:07: 15000000 INFO @ Sun, 21 Jun 2020 18:45:08: 9000000 INFO @ Sun, 21 Jun 2020 18:45:13: 10000000 INFO @ Sun, 21 Jun 2020 18:45:13: 16000000 INFO @ Sun, 21 Jun 2020 18:45:18: 11000000 INFO @ Sun, 21 Jun 2020 18:45:18: 17000000 INFO @ Sun, 21 Jun 2020 18:45:23: 12000000 INFO @ Sun, 21 Jun 2020 18:45:23: 18000000 INFO @ Sun, 21 Jun 2020 18:45:24: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:45:24: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:45:24: #1 total tags in treatment: 18125749 INFO @ Sun, 21 Jun 2020 18:45:24: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:24: #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 18:45:25: #1 tags after filtering in treatment: 18125664 INFO @ Sun, 21 Jun 2020 18:45:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:45:25: #1 finished! INFO @ Sun, 21 Jun 2020 18:45:25: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:45:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:26: #2 number of paired peaks: 570 WARNING @ Sun, 21 Jun 2020 18:45:26: Fewer paired peaks (570) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 570 pairs to build model! INFO @ Sun, 21 Jun 2020 18:45:26: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:26: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:26: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:26: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:26: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 18:45:26: #2 alternative fragment length(s) may be 3,50,587 bps INFO @ Sun, 21 Jun 2020 18:45:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.10_model.r WARNING @ Sun, 21 Jun 2020 18:45:26: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:45:26: #2 You may need to consider one of the other alternative d(s): 3,50,587 WARNING @ Sun, 21 Jun 2020 18:45:26: #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 18:45:26: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:45:28: 13000000 INFO @ Sun, 21 Jun 2020 18:45:33: 14000000 INFO @ Sun, 21 Jun 2020 18:45:36: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:45:38: 15000000 INFO @ Sun, 21 Jun 2020 18:45:44: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 18:45:49: 17000000 INFO @ Sun, 21 Jun 2020 18:45:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.05_peaks.xls INFO @ Sun, 21 Jun 2020 18:45:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:45:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.05_summits.bed INFO @ Sun, 21 Jun 2020 18:45:52: Done! pass1 - making usageList (666 chroms): 1 millis pass2 - checking and writing primary data (3505 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 18:45:54: 18000000 INFO @ Sun, 21 Jun 2020 18:45:55: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 18:45:55: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 18:45:55: #1 total tags in treatment: 18125749 INFO @ Sun, 21 Jun 2020 18:45:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 18:45:55: #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 18:45:55: #1 tags after filtering in treatment: 18125664 INFO @ Sun, 21 Jun 2020 18:45:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 18:45:55: #1 finished! INFO @ Sun, 21 Jun 2020 18:45:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 18:45:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 18:45:56: #2 number of paired peaks: 570 WARNING @ Sun, 21 Jun 2020 18:45:56: Fewer paired peaks (570) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 570 pairs to build model! INFO @ Sun, 21 Jun 2020 18:45:56: start model_add_line... INFO @ Sun, 21 Jun 2020 18:45:56: start X-correlation... INFO @ Sun, 21 Jun 2020 18:45:56: end of X-cor INFO @ Sun, 21 Jun 2020 18:45:56: #2 finished! INFO @ Sun, 21 Jun 2020 18:45:56: #2 predicted fragment length is 50 bps INFO @ Sun, 21 Jun 2020 18:45:56: #2 alternative fragment length(s) may be 3,50,587 bps INFO @ Sun, 21 Jun 2020 18:45:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.20_model.r WARNING @ Sun, 21 Jun 2020 18:45:56: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 18:45:56: #2 You may need to consider one of the other alternative d(s): 3,50,587 WARNING @ Sun, 21 Jun 2020 18:45:56: #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 18:45:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 18:45:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 18:46:03: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.10_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.10_summits.bed INFO @ Sun, 21 Jun 2020 18:46:22: Done! pass1 - making usageList (459 chroms): 1 millis pass2 - checking and writing primary data (1463 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 18:46:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 18:46:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.20_peaks.xls INFO @ Sun, 21 Jun 2020 18:46:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 18:46:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2583185/SRX2583185.20_summits.bed INFO @ Sun, 21 Jun 2020 18:46:49: Done! pass1 - making usageList (188 chroms): 1 millis pass2 - checking and writing primary data (470 records, 4 fields): 6 millis CompletedMACS2peakCalling