Job ID = 6452526 SRX = SRX016141 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T07:48:01 prefetch.2.10.7: 1) Downloading 'SRR034692'... 2020-06-21T07:48:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T07:50:13 prefetch.2.10.7: HTTPS download succeed 2020-06-21T07:50:14 prefetch.2.10.7: 'SRR034692' is valid 2020-06-21T07:50:14 prefetch.2.10.7: 1) 'SRR034692' was downloaded successfully Read 16502467 spots for SRR034692/SRR034692.sra Written 16502467 spots for SRR034692/SRR034692.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: 00:02:39 16502467 reads; of these: 16502467 (100.00%) were unpaired; of these: 3480500 (21.09%) aligned 0 times 11679769 (70.78%) aligned exactly 1 time 1342198 (8.13%) aligned >1 times 78.91% overall alignment rate Time searching: 00:02:40 Overall time: 00:02:40 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_rmdupse_core] 1959005 / 13021967 = 0.1504 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 16:57:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.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 16:57:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:57:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:57:06: 1000000 INFO @ Sun, 21 Jun 2020 16:57:11: 2000000 INFO @ Sun, 21 Jun 2020 16:57:16: 3000000 INFO @ Sun, 21 Jun 2020 16:57:20: 4000000 INFO @ Sun, 21 Jun 2020 16:57:25: 5000000 INFO @ Sun, 21 Jun 2020 16:57:30: 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 16:57:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.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 16:57:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:57:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:57:34: 7000000 INFO @ Sun, 21 Jun 2020 16:57:37: 1000000 INFO @ Sun, 21 Jun 2020 16:57:39: 8000000 INFO @ Sun, 21 Jun 2020 16:57:43: 2000000 INFO @ Sun, 21 Jun 2020 16:57:44: 9000000 INFO @ Sun, 21 Jun 2020 16:57:48: 3000000 INFO @ Sun, 21 Jun 2020 16:57:49: 10000000 INFO @ Sun, 21 Jun 2020 16:57:53: 4000000 INFO @ Sun, 21 Jun 2020 16:57:54: 11000000 INFO @ Sun, 21 Jun 2020 16:57:54: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:57:54: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:57:54: #1 total tags in treatment: 11062962 INFO @ Sun, 21 Jun 2020 16:57:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:57:54: #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 16:57:55: #1 tags after filtering in treatment: 11062790 INFO @ Sun, 21 Jun 2020 16:57:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:57:55: #1 finished! INFO @ Sun, 21 Jun 2020 16:57:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:57:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:57:55: #2 number of paired peaks: 113 WARNING @ Sun, 21 Jun 2020 16:57:55: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Sun, 21 Jun 2020 16:57:55: start model_add_line... INFO @ Sun, 21 Jun 2020 16:57:55: start X-correlation... INFO @ Sun, 21 Jun 2020 16:57:55: end of X-cor INFO @ Sun, 21 Jun 2020 16:57:55: #2 finished! INFO @ Sun, 21 Jun 2020 16:57:55: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 16:57:55: #2 alternative fragment length(s) may be 63 bps INFO @ Sun, 21 Jun 2020 16:57:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.05_model.r WARNING @ Sun, 21 Jun 2020 16:57:55: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:57:55: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Sun, 21 Jun 2020 16:57:55: #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 16:57:55: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:57:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:57:58: 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 16:58:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.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 16:58:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 16:58:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 16:58:03: 6000000 INFO @ Sun, 21 Jun 2020 16:58:07: 1000000 INFO @ Sun, 21 Jun 2020 16:58:09: 7000000 INFO @ Sun, 21 Jun 2020 16:58:11: 2000000 INFO @ Sun, 21 Jun 2020 16:58:14: 8000000 INFO @ Sun, 21 Jun 2020 16:58:16: 3000000 INFO @ Sun, 21 Jun 2020 16:58:17: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:58:20: 9000000 INFO @ Sun, 21 Jun 2020 16:58:21: 4000000 INFO @ Sun, 21 Jun 2020 16:58:25: 10000000 INFO @ Sun, 21 Jun 2020 16:58:26: 5000000 INFO @ Sun, 21 Jun 2020 16:58:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.05_peaks.xls INFO @ Sun, 21 Jun 2020 16:58:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:58:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.05_summits.bed INFO @ Sun, 21 Jun 2020 16:58:28: Done! pass1 - making usageList (87 chroms): 1 millis pass2 - checking and writing primary data (655 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 16:58:30: 11000000 INFO @ Sun, 21 Jun 2020 16:58:30: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:58:30: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:58:30: #1 total tags in treatment: 11062962 INFO @ Sun, 21 Jun 2020 16:58:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:58:30: #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 16:58:31: 6000000 INFO @ Sun, 21 Jun 2020 16:58:31: #1 tags after filtering in treatment: 11062790 INFO @ Sun, 21 Jun 2020 16:58:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:58:31: #1 finished! INFO @ Sun, 21 Jun 2020 16:58:31: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:58:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:58:32: #2 number of paired peaks: 113 WARNING @ Sun, 21 Jun 2020 16:58:32: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Sun, 21 Jun 2020 16:58:32: start model_add_line... INFO @ Sun, 21 Jun 2020 16:58:32: start X-correlation... INFO @ Sun, 21 Jun 2020 16:58:32: end of X-cor INFO @ Sun, 21 Jun 2020 16:58:32: #2 finished! INFO @ Sun, 21 Jun 2020 16:58:32: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 16:58:32: #2 alternative fragment length(s) may be 63 bps INFO @ Sun, 21 Jun 2020 16:58:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.10_model.r WARNING @ Sun, 21 Jun 2020 16:58:32: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:58:32: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Sun, 21 Jun 2020 16:58:32: #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 16:58:32: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:58:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:58:35: 7000000 INFO @ Sun, 21 Jun 2020 16:58:40: 8000000 INFO @ Sun, 21 Jun 2020 16:58:45: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 16:58:49: 10000000 INFO @ Sun, 21 Jun 2020 16:58:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:58:54: 11000000 INFO @ Sun, 21 Jun 2020 16:58:54: #1 tag size is determined as 36 bps INFO @ Sun, 21 Jun 2020 16:58:54: #1 tag size = 36 INFO @ Sun, 21 Jun 2020 16:58:54: #1 total tags in treatment: 11062962 INFO @ Sun, 21 Jun 2020 16:58:54: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 16:58:54: #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 16:58:55: #1 tags after filtering in treatment: 11062790 INFO @ Sun, 21 Jun 2020 16:58:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 16:58:55: #1 finished! INFO @ Sun, 21 Jun 2020 16:58:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 16:58:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 16:58:55: #2 number of paired peaks: 113 WARNING @ Sun, 21 Jun 2020 16:58:55: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Sun, 21 Jun 2020 16:58:55: start model_add_line... INFO @ Sun, 21 Jun 2020 16:58:56: start X-correlation... INFO @ Sun, 21 Jun 2020 16:58:56: end of X-cor INFO @ Sun, 21 Jun 2020 16:58:56: #2 finished! INFO @ Sun, 21 Jun 2020 16:58:56: #2 predicted fragment length is 63 bps INFO @ Sun, 21 Jun 2020 16:58:56: #2 alternative fragment length(s) may be 63 bps INFO @ Sun, 21 Jun 2020 16:58:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.20_model.r WARNING @ Sun, 21 Jun 2020 16:58:56: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 16:58:56: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Sun, 21 Jun 2020 16:58:56: #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 16:58:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 16:58:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 16:59:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.10_peaks.xls INFO @ Sun, 21 Jun 2020 16:59:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:59:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.10_summits.bed INFO @ Sun, 21 Jun 2020 16:59:05: Done! pass1 - making usageList (60 chroms): 1 millis pass2 - checking and writing primary data (162 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 16:59:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 16:59:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.20_peaks.xls INFO @ Sun, 21 Jun 2020 16:59:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 16:59:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX016141/SRX016141.20_summits.bed INFO @ Sun, 21 Jun 2020 16:59:30: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (62 records, 4 fields): 3 millis CompletedMACS2peakCalling