Job ID = 6457089 SRX = SRX4375849 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:30:43 prefetch.2.10.7: 1) Downloading 'SRR7506503'... 2020-06-21T11:30:43 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:32:16 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:32:16 prefetch.2.10.7: 'SRR7506503' is valid 2020-06-21T11:32:16 prefetch.2.10.7: 1) 'SRR7506503' was downloaded successfully Read 10409128 spots for SRR7506503/SRR7506503.sra Written 10409128 spots for SRR7506503/SRR7506503.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: 00:02:17 10409128 reads; of these: 10409128 (100.00%) were unpaired; of these: 2361216 (22.68%) aligned 0 times 6367991 (61.18%) aligned exactly 1 time 1679921 (16.14%) aligned >1 times 77.32% overall alignment rate Time searching: 00:02:17 Overall time: 00:02:17 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] 860637 / 8047912 = 0.1069 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 20:38:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.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 20:38:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:38:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:38:36: 1000000 INFO @ Sun, 21 Jun 2020 20:38:44: 2000000 INFO @ Sun, 21 Jun 2020 20:38:52: 3000000 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 20:38:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.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 20:38:56: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:38:56: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:39:01: 4000000 INFO @ Sun, 21 Jun 2020 20:39:05: 1000000 INFO @ Sun, 21 Jun 2020 20:39:10: 5000000 INFO @ Sun, 21 Jun 2020 20:39:14: 2000000 INFO @ Sun, 21 Jun 2020 20:39:19: 6000000 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 20:39:24: 3000000 INFO @ Sun, 21 Jun 2020 20:39:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.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 20:39:26: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:39:26: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:39:28: 7000000 INFO @ Sun, 21 Jun 2020 20:39:30: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:39:30: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:39:30: #1 total tags in treatment: 7187275 INFO @ Sun, 21 Jun 2020 20:39:30: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:39:30: #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 20:39:30: #1 tags after filtering in treatment: 7187070 INFO @ Sun, 21 Jun 2020 20:39:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:39:30: #1 finished! INFO @ Sun, 21 Jun 2020 20:39:30: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:39:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:39:31: #2 number of paired peaks: 435 WARNING @ Sun, 21 Jun 2020 20:39:31: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Sun, 21 Jun 2020 20:39:31: start model_add_line... INFO @ Sun, 21 Jun 2020 20:39:31: start X-correlation... INFO @ Sun, 21 Jun 2020 20:39:31: end of X-cor INFO @ Sun, 21 Jun 2020 20:39:31: #2 finished! INFO @ Sun, 21 Jun 2020 20:39:31: #2 predicted fragment length is 94 bps INFO @ Sun, 21 Jun 2020 20:39:31: #2 alternative fragment length(s) may be 94 bps INFO @ Sun, 21 Jun 2020 20:39:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.05_model.r WARNING @ Sun, 21 Jun 2020 20:39:31: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:39:31: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sun, 21 Jun 2020 20:39:31: #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 20:39:31: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:39:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:39:33: 4000000 INFO @ Sun, 21 Jun 2020 20:39:35: 1000000 INFO @ Sun, 21 Jun 2020 20:39:43: 5000000 INFO @ Sun, 21 Jun 2020 20:39:44: 2000000 INFO @ Sun, 21 Jun 2020 20:39:46: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:39:53: 3000000 INFO @ Sun, 21 Jun 2020 20:39:54: 6000000 INFO @ Sun, 21 Jun 2020 20:39:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:39:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:39:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.05_summits.bed INFO @ Sun, 21 Jun 2020 20:39:55: Done! pass1 - making usageList (348 chroms): 1 millis pass2 - checking and writing primary data (2181 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:40:02: 4000000 INFO @ Sun, 21 Jun 2020 20:40:05: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:40:07: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:40:07: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:40:07: #1 total tags in treatment: 7187275 INFO @ Sun, 21 Jun 2020 20:40:07: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:40:07: #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 20:40:08: #1 tags after filtering in treatment: 7187070 INFO @ Sun, 21 Jun 2020 20:40:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:40:08: #1 finished! INFO @ Sun, 21 Jun 2020 20:40:08: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:40:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:40:09: #2 number of paired peaks: 435 WARNING @ Sun, 21 Jun 2020 20:40:09: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Sun, 21 Jun 2020 20:40:09: start model_add_line... INFO @ Sun, 21 Jun 2020 20:40:09: start X-correlation... INFO @ Sun, 21 Jun 2020 20:40:09: end of X-cor INFO @ Sun, 21 Jun 2020 20:40:09: #2 finished! INFO @ Sun, 21 Jun 2020 20:40:09: #2 predicted fragment length is 94 bps INFO @ Sun, 21 Jun 2020 20:40:09: #2 alternative fragment length(s) may be 94 bps INFO @ Sun, 21 Jun 2020 20:40:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.10_model.r WARNING @ Sun, 21 Jun 2020 20:40:09: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:40:09: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sun, 21 Jun 2020 20:40:09: #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 20:40:09: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:40:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:40:11: 5000000 INFO @ Sun, 21 Jun 2020 20:40:21: 6000000 INFO @ Sun, 21 Jun 2020 20:40:24: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:40:31: 7000000 INFO @ Sun, 21 Jun 2020 20:40:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:40:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:40:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.10_summits.bed INFO @ Sun, 21 Jun 2020 20:40:33: Done! INFO @ Sun, 21 Jun 2020 20:40:33: #1 tag size is determined as 51 bps INFO @ Sun, 21 Jun 2020 20:40:33: #1 tag size = 51 INFO @ Sun, 21 Jun 2020 20:40:33: #1 total tags in treatment: 7187275 INFO @ Sun, 21 Jun 2020 20:40:33: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:40:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (214 chroms): 2 millis pass2 - checking and writing primary data (647 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:40:34: #1 tags after filtering in treatment: 7187070 INFO @ Sun, 21 Jun 2020 20:40:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:40:34: #1 finished! INFO @ Sun, 21 Jun 2020 20:40:34: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:40:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:40:34: #2 number of paired peaks: 435 WARNING @ Sun, 21 Jun 2020 20:40:34: Fewer paired peaks (435) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 435 pairs to build model! INFO @ Sun, 21 Jun 2020 20:40:34: start model_add_line... INFO @ Sun, 21 Jun 2020 20:40:34: start X-correlation... INFO @ Sun, 21 Jun 2020 20:40:34: end of X-cor INFO @ Sun, 21 Jun 2020 20:40:34: #2 finished! INFO @ Sun, 21 Jun 2020 20:40:34: #2 predicted fragment length is 94 bps INFO @ Sun, 21 Jun 2020 20:40:34: #2 alternative fragment length(s) may be 94 bps INFO @ Sun, 21 Jun 2020 20:40:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.20_model.r WARNING @ Sun, 21 Jun 2020 20:40:34: #2 Since the d (94) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:40:34: #2 You may need to consider one of the other alternative d(s): 94 WARNING @ Sun, 21 Jun 2020 20:40:34: #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 20:40:34: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:40:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:40:49: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:40:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:40:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:40:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4375849/SRX4375849.20_summits.bed INFO @ Sun, 21 Jun 2020 20:40:58: Done! pass1 - making usageList (79 chroms): 1 millis pass2 - checking and writing primary data (179 records, 4 fields): 5 millis CompletedMACS2peakCalling