Job ID = 6527493 SRX = SRX032124 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:36:12 prefetch.2.10.7: 1) Downloading 'SRR073949'... 2020-06-29T12:36:12 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:37:32 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:37:33 prefetch.2.10.7: 'SRR073949' is valid 2020-06-29T12:37:33 prefetch.2.10.7: 1) 'SRR073949' was downloaded successfully Read 15188996 spots for SRR073949/SRR073949.sra Written 15188996 spots for SRR073949/SRR073949.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: 00:03:24 15188996 reads; of these: 15188996 (100.00%) were unpaired; of these: 1464949 (9.64%) aligned 0 times 11373225 (74.88%) aligned exactly 1 time 2350822 (15.48%) aligned >1 times 90.36% overall alignment rate Time searching: 00:03:25 Overall time: 00:03:25 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_rmdupse_core] 1579567 / 13724047 = 0.1151 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 21:47:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.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 21:47:42: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:47:42: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:47:49: 1000000 INFO @ Mon, 29 Jun 2020 21:47:55: 2000000 INFO @ Mon, 29 Jun 2020 21:48:02: 3000000 INFO @ Mon, 29 Jun 2020 21:48:08: 4000000 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 21:48:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.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 21:48:12: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:48:12: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:48:15: 5000000 INFO @ Mon, 29 Jun 2020 21:48:19: 1000000 INFO @ Mon, 29 Jun 2020 21:48:22: 6000000 INFO @ Mon, 29 Jun 2020 21:48:26: 2000000 INFO @ Mon, 29 Jun 2020 21:48:28: 7000000 INFO @ Mon, 29 Jun 2020 21:48:33: 3000000 INFO @ Mon, 29 Jun 2020 21:48:35: 8000000 INFO @ Mon, 29 Jun 2020 21:48:40: 4000000 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 21:48:42: 9000000 INFO @ Mon, 29 Jun 2020 21:48:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.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 21:48:42: #1 read tag files... INFO @ Mon, 29 Jun 2020 21:48:42: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 21:48:47: 5000000 INFO @ Mon, 29 Jun 2020 21:48:49: 10000000 INFO @ Mon, 29 Jun 2020 21:48:49: 1000000 INFO @ Mon, 29 Jun 2020 21:48:54: 6000000 INFO @ Mon, 29 Jun 2020 21:48:55: 2000000 INFO @ Mon, 29 Jun 2020 21:48:56: 11000000 INFO @ Mon, 29 Jun 2020 21:49:01: 7000000 INFO @ Mon, 29 Jun 2020 21:49:02: 3000000 INFO @ Mon, 29 Jun 2020 21:49:02: 12000000 INFO @ Mon, 29 Jun 2020 21:49:03: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 21:49:03: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 21:49:03: #1 total tags in treatment: 12144480 INFO @ Mon, 29 Jun 2020 21:49:03: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:49:03: #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 21:49:04: #1 tags after filtering in treatment: 12144480 INFO @ Mon, 29 Jun 2020 21:49:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:49:04: #1 finished! INFO @ Mon, 29 Jun 2020 21:49:04: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:49:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:49:04: #2 number of paired peaks: 114 WARNING @ Mon, 29 Jun 2020 21:49:04: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Mon, 29 Jun 2020 21:49:04: start model_add_line... INFO @ Mon, 29 Jun 2020 21:49:04: start X-correlation... INFO @ Mon, 29 Jun 2020 21:49:04: end of X-cor INFO @ Mon, 29 Jun 2020 21:49:04: #2 finished! INFO @ Mon, 29 Jun 2020 21:49:04: #2 predicted fragment length is 36 bps INFO @ Mon, 29 Jun 2020 21:49:04: #2 alternative fragment length(s) may be 36 bps INFO @ Mon, 29 Jun 2020 21:49:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.05_model.r WARNING @ Mon, 29 Jun 2020 21:49:04: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:49:04: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Mon, 29 Jun 2020 21:49:04: #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 21:49:04: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:49:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:49:07: 8000000 INFO @ Mon, 29 Jun 2020 21:49:08: 4000000 INFO @ Mon, 29 Jun 2020 21:49:14: 9000000 INFO @ Mon, 29 Jun 2020 21:49:15: 5000000 INFO @ Mon, 29 Jun 2020 21:49:21: 6000000 INFO @ Mon, 29 Jun 2020 21:49:21: 10000000 INFO @ Mon, 29 Jun 2020 21:49:27: 7000000 INFO @ Mon, 29 Jun 2020 21:49:28: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:49:28: 11000000 INFO @ Mon, 29 Jun 2020 21:49:34: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 21:49:35: 12000000 INFO @ Mon, 29 Jun 2020 21:49:36: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 21:49:36: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 21:49:36: #1 total tags in treatment: 12144480 INFO @ Mon, 29 Jun 2020 21:49:36: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:49:36: #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 21:49:36: #1 tags after filtering in treatment: 12144480 INFO @ Mon, 29 Jun 2020 21:49:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:49:36: #1 finished! INFO @ Mon, 29 Jun 2020 21:49:36: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:49:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:49:37: #2 number of paired peaks: 114 WARNING @ Mon, 29 Jun 2020 21:49:37: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Mon, 29 Jun 2020 21:49:37: start model_add_line... INFO @ Mon, 29 Jun 2020 21:49:37: start X-correlation... INFO @ Mon, 29 Jun 2020 21:49:37: end of X-cor INFO @ Mon, 29 Jun 2020 21:49:37: #2 finished! INFO @ Mon, 29 Jun 2020 21:49:37: #2 predicted fragment length is 36 bps INFO @ Mon, 29 Jun 2020 21:49:37: #2 alternative fragment length(s) may be 36 bps INFO @ Mon, 29 Jun 2020 21:49:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.10_model.r WARNING @ Mon, 29 Jun 2020 21:49:37: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:49:37: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Mon, 29 Jun 2020 21:49:37: #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 21:49:37: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:49:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:49:40: 9000000 INFO @ Mon, 29 Jun 2020 21:49:40: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.05_peaks.xls INFO @ Mon, 29 Jun 2020 21:49:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:49:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.05_summits.bed INFO @ Mon, 29 Jun 2020 21:49:40: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (741 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:49:45: 10000000 INFO @ Mon, 29 Jun 2020 21:49:51: 11000000 INFO @ Mon, 29 Jun 2020 21:49:56: 12000000 INFO @ Mon, 29 Jun 2020 21:49:57: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 21:49:57: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 21:49:57: #1 total tags in treatment: 12144480 INFO @ Mon, 29 Jun 2020 21:49:57: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 21:49:57: #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 21:49:57: #1 tags after filtering in treatment: 12144480 INFO @ Mon, 29 Jun 2020 21:49:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 21:49:57: #1 finished! INFO @ Mon, 29 Jun 2020 21:49:57: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 21:49:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 21:49:58: #2 number of paired peaks: 114 WARNING @ Mon, 29 Jun 2020 21:49:58: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Mon, 29 Jun 2020 21:49:58: start model_add_line... INFO @ Mon, 29 Jun 2020 21:49:58: start X-correlation... INFO @ Mon, 29 Jun 2020 21:49:58: end of X-cor INFO @ Mon, 29 Jun 2020 21:49:58: #2 finished! INFO @ Mon, 29 Jun 2020 21:49:58: #2 predicted fragment length is 36 bps INFO @ Mon, 29 Jun 2020 21:49:58: #2 alternative fragment length(s) may be 36 bps INFO @ Mon, 29 Jun 2020 21:49:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.20_model.r WARNING @ Mon, 29 Jun 2020 21:49:58: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 21:49:58: #2 You may need to consider one of the other alternative d(s): 36 WARNING @ Mon, 29 Jun 2020 21:49:58: #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 21:49:58: #3 Call peaks... INFO @ Mon, 29 Jun 2020 21:49:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 21:50:00: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 21:50:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.10_peaks.xls INFO @ Mon, 29 Jun 2020 21:50:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:50:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.10_summits.bed INFO @ Mon, 29 Jun 2020 21:50:12: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (547 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 21:50:22: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 21:50:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.20_peaks.xls INFO @ Mon, 29 Jun 2020 21:50:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 21:50:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX032124/SRX032124.20_summits.bed INFO @ Mon, 29 Jun 2020 21:50:34: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (377 records, 4 fields): 1 millis CompletedMACS2peakCalling