Job ID = 6527608 SRX = SRX1361350 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:42:46 prefetch.2.10.7: 1) Downloading 'SRR2749788'... 2020-06-29T12:42:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:45:50 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:45:50 prefetch.2.10.7: 1) 'SRR2749788' was downloaded successfully Read 27782670 spots for SRR2749788/SRR2749788.sra Written 27782670 spots for SRR2749788/SRR2749788.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: 00:14:55 27782670 reads; of these: 27782670 (100.00%) were unpaired; of these: 748443 (2.69%) aligned 0 times 11737910 (42.25%) aligned exactly 1 time 15296317 (55.06%) aligned >1 times 97.31% overall alignment rate Time searching: 00:14:55 Overall time: 00:14:55 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 12 files... [bam_rmdupse_core] 7574310 / 27034227 = 0.2802 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 22:18:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.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 22:18:44: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:18:44: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:18:51: 1000000 INFO @ Mon, 29 Jun 2020 22:18:59: 2000000 INFO @ Mon, 29 Jun 2020 22:19:06: 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 @ Mon, 29 Jun 2020 22:19:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.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 22:19:14: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:19:14: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:19:14: 4000000 INFO @ Mon, 29 Jun 2020 22:19:22: 5000000 INFO @ Mon, 29 Jun 2020 22:19:22: 1000000 INFO @ Mon, 29 Jun 2020 22:19:30: 6000000 INFO @ Mon, 29 Jun 2020 22:19:30: 2000000 INFO @ Mon, 29 Jun 2020 22:19:37: 7000000 INFO @ Mon, 29 Jun 2020 22:19:38: 3000000 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 22:19:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.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 22:19:44: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:19:44: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:19:45: 8000000 INFO @ Mon, 29 Jun 2020 22:19:46: 4000000 INFO @ Mon, 29 Jun 2020 22:19:53: 1000000 INFO @ Mon, 29 Jun 2020 22:19:53: 9000000 INFO @ Mon, 29 Jun 2020 22:19:55: 5000000 INFO @ Mon, 29 Jun 2020 22:20:01: 2000000 INFO @ Mon, 29 Jun 2020 22:20:01: 10000000 INFO @ Mon, 29 Jun 2020 22:20:03: 6000000 INFO @ Mon, 29 Jun 2020 22:20:09: 3000000 INFO @ Mon, 29 Jun 2020 22:20:09: 11000000 INFO @ Mon, 29 Jun 2020 22:20:11: 7000000 INFO @ Mon, 29 Jun 2020 22:20:17: 4000000 INFO @ Mon, 29 Jun 2020 22:20:18: 12000000 INFO @ Mon, 29 Jun 2020 22:20:19: 8000000 INFO @ Mon, 29 Jun 2020 22:20:25: 5000000 INFO @ Mon, 29 Jun 2020 22:20:26: 13000000 INFO @ Mon, 29 Jun 2020 22:20:27: 9000000 INFO @ Mon, 29 Jun 2020 22:20:33: 6000000 INFO @ Mon, 29 Jun 2020 22:20:34: 14000000 INFO @ Mon, 29 Jun 2020 22:20:35: 10000000 INFO @ Mon, 29 Jun 2020 22:20:41: 7000000 INFO @ Mon, 29 Jun 2020 22:20:43: 15000000 INFO @ Mon, 29 Jun 2020 22:20:44: 11000000 INFO @ Mon, 29 Jun 2020 22:20:49: 8000000 INFO @ Mon, 29 Jun 2020 22:20:51: 16000000 INFO @ Mon, 29 Jun 2020 22:20:52: 12000000 INFO @ Mon, 29 Jun 2020 22:20:57: 9000000 INFO @ Mon, 29 Jun 2020 22:20:59: 17000000 INFO @ Mon, 29 Jun 2020 22:21:00: 13000000 INFO @ Mon, 29 Jun 2020 22:21:05: 10000000 INFO @ Mon, 29 Jun 2020 22:21:07: 18000000 INFO @ Mon, 29 Jun 2020 22:21:08: 14000000 INFO @ Mon, 29 Jun 2020 22:21:13: 11000000 INFO @ Mon, 29 Jun 2020 22:21:15: 19000000 INFO @ Mon, 29 Jun 2020 22:21:17: 15000000 INFO @ Mon, 29 Jun 2020 22:21:19: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:21:19: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:21:19: #1 total tags in treatment: 19459917 INFO @ Mon, 29 Jun 2020 22:21:19: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:21:19: #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 22:21:20: #1 tags after filtering in treatment: 19459917 INFO @ Mon, 29 Jun 2020 22:21:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:21:20: #1 finished! INFO @ Mon, 29 Jun 2020 22:21:20: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:21:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:21:21: 12000000 INFO @ Mon, 29 Jun 2020 22:21:21: #2 number of paired peaks: 629 WARNING @ Mon, 29 Jun 2020 22:21:21: Fewer paired peaks (629) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 629 pairs to build model! INFO @ Mon, 29 Jun 2020 22:21:21: start model_add_line... INFO @ Mon, 29 Jun 2020 22:21:21: start X-correlation... INFO @ Mon, 29 Jun 2020 22:21:21: end of X-cor INFO @ Mon, 29 Jun 2020 22:21:21: #2 finished! INFO @ Mon, 29 Jun 2020 22:21:21: #2 predicted fragment length is 45 bps INFO @ Mon, 29 Jun 2020 22:21:21: #2 alternative fragment length(s) may be 4,45 bps INFO @ Mon, 29 Jun 2020 22:21:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.05_model.r WARNING @ Mon, 29 Jun 2020 22:21:21: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:21:21: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Mon, 29 Jun 2020 22:21:21: #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 22:21:21: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:21:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:21:25: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:21:29: 13000000 INFO @ Mon, 29 Jun 2020 22:21:32: 17000000 INFO @ Mon, 29 Jun 2020 22:21:37: 14000000 INFO @ Mon, 29 Jun 2020 22:21:40: 18000000 INFO @ Mon, 29 Jun 2020 22:21:45: 15000000 INFO @ Mon, 29 Jun 2020 22:21:47: 19000000 INFO @ Mon, 29 Jun 2020 22:21:51: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:21:51: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:21:51: #1 total tags in treatment: 19459917 INFO @ Mon, 29 Jun 2020 22:21:51: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:21:51: #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 22:21:51: #1 tags after filtering in treatment: 19459917 INFO @ Mon, 29 Jun 2020 22:21:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:21:51: #1 finished! INFO @ Mon, 29 Jun 2020 22:21:51: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:21:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:21:52: #2 number of paired peaks: 629 WARNING @ Mon, 29 Jun 2020 22:21:52: Fewer paired peaks (629) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 629 pairs to build model! INFO @ Mon, 29 Jun 2020 22:21:52: start model_add_line... INFO @ Mon, 29 Jun 2020 22:21:53: start X-correlation... INFO @ Mon, 29 Jun 2020 22:21:53: end of X-cor INFO @ Mon, 29 Jun 2020 22:21:53: #2 finished! INFO @ Mon, 29 Jun 2020 22:21:53: #2 predicted fragment length is 45 bps INFO @ Mon, 29 Jun 2020 22:21:53: #2 alternative fragment length(s) may be 4,45 bps INFO @ Mon, 29 Jun 2020 22:21:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.10_model.r WARNING @ Mon, 29 Jun 2020 22:21:53: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:21:53: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Mon, 29 Jun 2020 22:21:53: #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 22:21:53: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:21:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:21:53: 16000000 INFO @ Mon, 29 Jun 2020 22:21:58: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:22:01: 17000000 INFO @ Mon, 29 Jun 2020 22:22:09: 18000000 BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:22:17: 19000000 INFO @ Mon, 29 Jun 2020 22:22:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:22:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:22:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.05_summits.bed INFO @ Mon, 29 Jun 2020 22:22:18: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (10440 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:22:21: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:22:21: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:22:21: #1 total tags in treatment: 19459917 INFO @ Mon, 29 Jun 2020 22:22:21: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:22:21: #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 22:22:21: #1 tags after filtering in treatment: 19459917 INFO @ Mon, 29 Jun 2020 22:22:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:22:21: #1 finished! INFO @ Mon, 29 Jun 2020 22:22:21: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:22:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:22:22: #2 number of paired peaks: 629 WARNING @ Mon, 29 Jun 2020 22:22:22: Fewer paired peaks (629) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 629 pairs to build model! INFO @ Mon, 29 Jun 2020 22:22:22: start model_add_line... INFO @ Mon, 29 Jun 2020 22:22:23: start X-correlation... INFO @ Mon, 29 Jun 2020 22:22:23: end of X-cor INFO @ Mon, 29 Jun 2020 22:22:23: #2 finished! INFO @ Mon, 29 Jun 2020 22:22:23: #2 predicted fragment length is 45 bps INFO @ Mon, 29 Jun 2020 22:22:23: #2 alternative fragment length(s) may be 4,45 bps INFO @ Mon, 29 Jun 2020 22:22:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.20_model.r WARNING @ Mon, 29 Jun 2020 22:22:23: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:22:23: #2 You may need to consider one of the other alternative d(s): 4,45 WARNING @ Mon, 29 Jun 2020 22:22:23: #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 22:22:23: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:22:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:22:29: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:22:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:22:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:22:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.10_summits.bed INFO @ Mon, 29 Jun 2020 22:22:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2785 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:22:58: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:23:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:23:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:23:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1361350/SRX1361350.20_summits.bed INFO @ Mon, 29 Jun 2020 22:23:18: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1287 records, 4 fields): 4 millis CompletedMACS2peakCalling