Job ID = 6527495 SRX = SRX032127 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:36:13 prefetch.2.10.7: 1) Downloading 'SRR073953'... 2020-06-29T13:36:13 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:39:16 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:39:17 prefetch.2.10.7: 'SRR073953' is valid 2020-06-29T13:39:17 prefetch.2.10.7: 1) 'SRR073953' was downloaded successfully Read 15825369 spots for SRR073953/SRR073953.sra Written 15825369 spots for SRR073953/SRR073953.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: 00:03:07 15825369 reads; of these: 15825369 (100.00%) were unpaired; of these: 1887962 (11.93%) aligned 0 times 11843973 (74.84%) aligned exactly 1 time 2093434 (13.23%) aligned >1 times 88.07% overall alignment rate Time searching: 00:03:07 Overall time: 00:03:07 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] 869169 / 13937407 = 0.0624 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 22:51:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.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 22:51:42: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:51:42: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:51:47: 1000000 INFO @ Mon, 29 Jun 2020 22:51:52: 2000000 INFO @ Mon, 29 Jun 2020 22:51:57: 3000000 INFO @ Mon, 29 Jun 2020 22:52:02: 4000000 INFO @ Mon, 29 Jun 2020 22:52:07: 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 @ Mon, 29 Jun 2020 22:52:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.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 22:52:12: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:52:12: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:52:12: 6000000 INFO @ Mon, 29 Jun 2020 22:52:17: 1000000 INFO @ Mon, 29 Jun 2020 22:52:18: 7000000 INFO @ Mon, 29 Jun 2020 22:52:23: 8000000 INFO @ Mon, 29 Jun 2020 22:52:23: 2000000 INFO @ Mon, 29 Jun 2020 22:52:28: 9000000 INFO @ Mon, 29 Jun 2020 22:52:29: 3000000 INFO @ Mon, 29 Jun 2020 22:52:33: 10000000 INFO @ Mon, 29 Jun 2020 22:52:34: 4000000 INFO @ Mon, 29 Jun 2020 22:52:38: 11000000 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 22:52:39: 5000000 INFO @ Mon, 29 Jun 2020 22:52:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.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 22:52:42: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:52:42: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:52:44: 12000000 INFO @ Mon, 29 Jun 2020 22:52:45: 6000000 INFO @ Mon, 29 Jun 2020 22:52:48: 1000000 INFO @ Mon, 29 Jun 2020 22:52:50: 13000000 INFO @ Mon, 29 Jun 2020 22:52:50: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:52:50: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:52:50: #1 total tags in treatment: 13068238 INFO @ Mon, 29 Jun 2020 22:52:50: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:52:50: #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 22:52:50: #1 tags after filtering in treatment: 13068238 INFO @ Mon, 29 Jun 2020 22:52:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:52:50: #1 finished! INFO @ Mon, 29 Jun 2020 22:52:50: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:52:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:52:51: 7000000 INFO @ Mon, 29 Jun 2020 22:52:51: #2 number of paired peaks: 112 WARNING @ Mon, 29 Jun 2020 22:52:51: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Mon, 29 Jun 2020 22:52:51: start model_add_line... INFO @ Mon, 29 Jun 2020 22:52:51: start X-correlation... INFO @ Mon, 29 Jun 2020 22:52:51: end of X-cor INFO @ Mon, 29 Jun 2020 22:52:51: #2 finished! INFO @ Mon, 29 Jun 2020 22:52:51: #2 predicted fragment length is 35 bps INFO @ Mon, 29 Jun 2020 22:52:51: #2 alternative fragment length(s) may be 35 bps INFO @ Mon, 29 Jun 2020 22:52:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.05_model.r WARNING @ Mon, 29 Jun 2020 22:52:51: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:52:51: #2 You may need to consider one of the other alternative d(s): 35 WARNING @ Mon, 29 Jun 2020 22:52:51: #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 22:52:51: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:52:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:52:53: 2000000 INFO @ Mon, 29 Jun 2020 22:52:56: 8000000 INFO @ Mon, 29 Jun 2020 22:52:58: 3000000 INFO @ Mon, 29 Jun 2020 22:53:02: 9000000 INFO @ Mon, 29 Jun 2020 22:53:04: 4000000 INFO @ Mon, 29 Jun 2020 22:53:07: 10000000 INFO @ Mon, 29 Jun 2020 22:53:09: 5000000 INFO @ Mon, 29 Jun 2020 22:53:13: 11000000 INFO @ Mon, 29 Jun 2020 22:53:14: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:53:14: 6000000 INFO @ Mon, 29 Jun 2020 22:53:18: 12000000 INFO @ Mon, 29 Jun 2020 22:53:20: 7000000 INFO @ Mon, 29 Jun 2020 22:53:24: 13000000 INFO @ Mon, 29 Jun 2020 22:53:24: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:53:24: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:53:24: #1 total tags in treatment: 13068238 INFO @ Mon, 29 Jun 2020 22:53:24: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:53:24: #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 22:53:25: #1 tags after filtering in treatment: 13068238 INFO @ Mon, 29 Jun 2020 22:53:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:53:25: #1 finished! INFO @ Mon, 29 Jun 2020 22:53:25: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:53:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:53:25: 8000000 INFO @ Mon, 29 Jun 2020 22:53:26: #2 number of paired peaks: 112 WARNING @ Mon, 29 Jun 2020 22:53:26: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Mon, 29 Jun 2020 22:53:26: start model_add_line... INFO @ Mon, 29 Jun 2020 22:53:26: start X-correlation... INFO @ Mon, 29 Jun 2020 22:53:26: end of X-cor INFO @ Mon, 29 Jun 2020 22:53:26: #2 finished! INFO @ Mon, 29 Jun 2020 22:53:26: #2 predicted fragment length is 35 bps INFO @ Mon, 29 Jun 2020 22:53:26: #2 alternative fragment length(s) may be 35 bps INFO @ Mon, 29 Jun 2020 22:53:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.10_model.r WARNING @ Mon, 29 Jun 2020 22:53:26: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:53:26: #2 You may need to consider one of the other alternative d(s): 35 WARNING @ Mon, 29 Jun 2020 22:53:26: #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 22:53:26: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:53:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:53:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:53:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:53:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.05_summits.bed INFO @ Mon, 29 Jun 2020 22:53:26: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (639 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:53:30: 9000000 INFO @ Mon, 29 Jun 2020 22:53:35: 10000000 INFO @ Mon, 29 Jun 2020 22:53:41: 11000000 INFO @ Mon, 29 Jun 2020 22:53:46: 12000000 INFO @ Mon, 29 Jun 2020 22:53:48: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:53:51: 13000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:53:51: #1 tag size is determined as 36 bps INFO @ Mon, 29 Jun 2020 22:53:51: #1 tag size = 36 INFO @ Mon, 29 Jun 2020 22:53:51: #1 total tags in treatment: 13068238 INFO @ Mon, 29 Jun 2020 22:53:51: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:53:51: #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 22:53:52: #1 tags after filtering in treatment: 13068238 INFO @ Mon, 29 Jun 2020 22:53:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:53:52: #1 finished! INFO @ Mon, 29 Jun 2020 22:53:52: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:53:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:53:53: #2 number of paired peaks: 112 WARNING @ Mon, 29 Jun 2020 22:53:53: Fewer paired peaks (112) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 112 pairs to build model! INFO @ Mon, 29 Jun 2020 22:53:53: start model_add_line... INFO @ Mon, 29 Jun 2020 22:53:53: start X-correlation... INFO @ Mon, 29 Jun 2020 22:53:53: end of X-cor INFO @ Mon, 29 Jun 2020 22:53:53: #2 finished! INFO @ Mon, 29 Jun 2020 22:53:53: #2 predicted fragment length is 35 bps INFO @ Mon, 29 Jun 2020 22:53:53: #2 alternative fragment length(s) may be 35 bps INFO @ Mon, 29 Jun 2020 22:53:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.20_model.r WARNING @ Mon, 29 Jun 2020 22:53:53: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:53:53: #2 You may need to consider one of the other alternative d(s): 35 WARNING @ Mon, 29 Jun 2020 22:53:53: #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 22:53:53: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:53:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:54:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:54:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:54:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.10_summits.bed INFO @ Mon, 29 Jun 2020 22:54:01: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (431 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:54:15: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:54:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:54:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:54:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX032127/SRX032127.20_summits.bed INFO @ Mon, 29 Jun 2020 22:54:27: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (340 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。