Job ID = 6527424 SRX = ERX1266821 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T12:39:11 prefetch.2.10.7: 1) Downloading 'ERR1193503'... 2020-06-29T12:39:11 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:40:43 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:40:44 prefetch.2.10.7: 'ERR1193503' is valid 2020-06-29T12:40:44 prefetch.2.10.7: 1) 'ERR1193503' was downloaded successfully Read 13569277 spots for ERR1193503/ERR1193503.sra Written 13569277 spots for ERR1193503/ERR1193503.sra 2020-06-29T12:41:36 prefetch.2.10.7: 1) Downloading 'ERR1193510'... 2020-06-29T12:41:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T12:43:14 prefetch.2.10.7: HTTPS download succeed 2020-06-29T12:43:14 prefetch.2.10.7: 'ERR1193510' is valid 2020-06-29T12:43:14 prefetch.2.10.7: 1) 'ERR1193510' was downloaded successfully Read 13013183 spots for ERR1193510/ERR1193510.sra Written 13013183 spots for ERR1193510/ERR1193510.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: 00:09:43 26582460 reads; of these: 26582460 (100.00%) were unpaired; of these: 2977889 (11.20%) aligned 0 times 14327595 (53.90%) aligned exactly 1 time 9276976 (34.90%) aligned >1 times 88.80% overall alignment rate Time searching: 00:09:43 Overall time: 00:09:43 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 8 files... [bam_rmdupse_core] 4418638 / 23604571 = 0.1872 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 22:06:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.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 22:06:11: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:06:11: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:06:17: 1000000 INFO @ Mon, 29 Jun 2020 22:06:22: 2000000 INFO @ Mon, 29 Jun 2020 22:06:28: 3000000 INFO @ Mon, 29 Jun 2020 22:06:33: 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 22:06:39: 5000000 INFO @ Mon, 29 Jun 2020 22:06:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.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 22:06:40: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:06:40: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:06:44: 6000000 INFO @ Mon, 29 Jun 2020 22:06:46: 1000000 INFO @ Mon, 29 Jun 2020 22:06:50: 7000000 INFO @ Mon, 29 Jun 2020 22:06:52: 2000000 INFO @ Mon, 29 Jun 2020 22:06:56: 8000000 INFO @ Mon, 29 Jun 2020 22:06:58: 3000000 INFO @ Mon, 29 Jun 2020 22:07:02: 9000000 INFO @ Mon, 29 Jun 2020 22:07:04: 4000000 INFO @ Mon, 29 Jun 2020 22:07:08: 10000000 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 22:07:10: 5000000 INFO @ Mon, 29 Jun 2020 22:07:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.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 22:07:10: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:07:10: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:07:13: 11000000 INFO @ Mon, 29 Jun 2020 22:07:16: 6000000 INFO @ Mon, 29 Jun 2020 22:07:16: 1000000 INFO @ Mon, 29 Jun 2020 22:07:19: 12000000 INFO @ Mon, 29 Jun 2020 22:07:22: 7000000 INFO @ Mon, 29 Jun 2020 22:07:23: 2000000 INFO @ Mon, 29 Jun 2020 22:07:25: 13000000 INFO @ Mon, 29 Jun 2020 22:07:28: 8000000 INFO @ Mon, 29 Jun 2020 22:07:28: 3000000 INFO @ Mon, 29 Jun 2020 22:07:31: 14000000 INFO @ Mon, 29 Jun 2020 22:07:34: 9000000 INFO @ Mon, 29 Jun 2020 22:07:34: 4000000 INFO @ Mon, 29 Jun 2020 22:07:37: 15000000 INFO @ Mon, 29 Jun 2020 22:07:40: 10000000 INFO @ Mon, 29 Jun 2020 22:07:40: 5000000 INFO @ Mon, 29 Jun 2020 22:07:43: 16000000 INFO @ Mon, 29 Jun 2020 22:07:46: 11000000 INFO @ Mon, 29 Jun 2020 22:07:46: 6000000 INFO @ Mon, 29 Jun 2020 22:07:49: 17000000 INFO @ Mon, 29 Jun 2020 22:07:52: 12000000 INFO @ Mon, 29 Jun 2020 22:07:52: 7000000 INFO @ Mon, 29 Jun 2020 22:07:55: 18000000 INFO @ Mon, 29 Jun 2020 22:07:58: 13000000 INFO @ Mon, 29 Jun 2020 22:07:58: 8000000 INFO @ Mon, 29 Jun 2020 22:08:01: 19000000 INFO @ Mon, 29 Jun 2020 22:08:02: #1 tag size is determined as 44 bps INFO @ Mon, 29 Jun 2020 22:08:02: #1 tag size = 44 INFO @ Mon, 29 Jun 2020 22:08:02: #1 total tags in treatment: 19185933 INFO @ Mon, 29 Jun 2020 22:08:02: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:08:02: #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 22:08:03: #1 tags after filtering in treatment: 19185933 INFO @ Mon, 29 Jun 2020 22:08:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:08:03: #1 finished! INFO @ Mon, 29 Jun 2020 22:08:03: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:08:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:08:04: #2 number of paired peaks: 176 WARNING @ Mon, 29 Jun 2020 22:08:04: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Mon, 29 Jun 2020 22:08:04: start model_add_line... INFO @ Mon, 29 Jun 2020 22:08:04: start X-correlation... INFO @ Mon, 29 Jun 2020 22:08:04: end of X-cor INFO @ Mon, 29 Jun 2020 22:08:04: #2 finished! INFO @ Mon, 29 Jun 2020 22:08:04: #2 predicted fragment length is 40 bps INFO @ Mon, 29 Jun 2020 22:08:04: #2 alternative fragment length(s) may be 40 bps INFO @ Mon, 29 Jun 2020 22:08:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.05_model.r WARNING @ Mon, 29 Jun 2020 22:08:04: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:08:04: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Mon, 29 Jun 2020 22:08:04: #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 22:08:04: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:08:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:08:04: 14000000 INFO @ Mon, 29 Jun 2020 22:08:04: 9000000 INFO @ Mon, 29 Jun 2020 22:08:10: 15000000 INFO @ Mon, 29 Jun 2020 22:08:11: 10000000 INFO @ Mon, 29 Jun 2020 22:08:17: 16000000 INFO @ Mon, 29 Jun 2020 22:08:17: 11000000 INFO @ Mon, 29 Jun 2020 22:08:23: 17000000 INFO @ Mon, 29 Jun 2020 22:08:23: 12000000 INFO @ Mon, 29 Jun 2020 22:08:29: 18000000 INFO @ Mon, 29 Jun 2020 22:08:29: 13000000 INFO @ Mon, 29 Jun 2020 22:08:35: 19000000 INFO @ Mon, 29 Jun 2020 22:08:35: 14000000 INFO @ Mon, 29 Jun 2020 22:08:36: #1 tag size is determined as 44 bps INFO @ Mon, 29 Jun 2020 22:08:36: #1 tag size = 44 INFO @ Mon, 29 Jun 2020 22:08:36: #1 total tags in treatment: 19185933 INFO @ Mon, 29 Jun 2020 22:08:36: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:08:36: #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 22:08:36: #1 tags after filtering in treatment: 19185933 INFO @ Mon, 29 Jun 2020 22:08:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:08:36: #1 finished! INFO @ Mon, 29 Jun 2020 22:08:36: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:08:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:08:38: #2 number of paired peaks: 176 WARNING @ Mon, 29 Jun 2020 22:08:38: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Mon, 29 Jun 2020 22:08:38: start model_add_line... INFO @ Mon, 29 Jun 2020 22:08:38: start X-correlation... INFO @ Mon, 29 Jun 2020 22:08:38: end of X-cor INFO @ Mon, 29 Jun 2020 22:08:38: #2 finished! INFO @ Mon, 29 Jun 2020 22:08:38: #2 predicted fragment length is 40 bps INFO @ Mon, 29 Jun 2020 22:08:38: #2 alternative fragment length(s) may be 40 bps INFO @ Mon, 29 Jun 2020 22:08:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.10_model.r WARNING @ Mon, 29 Jun 2020 22:08:38: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:08:38: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Mon, 29 Jun 2020 22:08:38: #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 22:08:38: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:08:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:08:41: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:08:46: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:08:48: 16000000 INFO @ Mon, 29 Jun 2020 22:08:54: 17000000 INFO @ Mon, 29 Jun 2020 22:09:00: 18000000 INFO @ Mon, 29 Jun 2020 22:09:06: 19000000 INFO @ Mon, 29 Jun 2020 22:09:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:09:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:09:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.05_summits.bed INFO @ Mon, 29 Jun 2020 22:09:07: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1960 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:09:07: #1 tag size is determined as 44 bps INFO @ Mon, 29 Jun 2020 22:09:07: #1 tag size = 44 INFO @ Mon, 29 Jun 2020 22:09:07: #1 total tags in treatment: 19185933 INFO @ Mon, 29 Jun 2020 22:09:07: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:09:07: #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 22:09:07: #1 tags after filtering in treatment: 19185933 INFO @ Mon, 29 Jun 2020 22:09:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:09:07: #1 finished! INFO @ Mon, 29 Jun 2020 22:09:07: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:09:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:09:09: #2 number of paired peaks: 176 WARNING @ Mon, 29 Jun 2020 22:09:09: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Mon, 29 Jun 2020 22:09:09: start model_add_line... INFO @ Mon, 29 Jun 2020 22:09:09: start X-correlation... INFO @ Mon, 29 Jun 2020 22:09:09: end of X-cor INFO @ Mon, 29 Jun 2020 22:09:09: #2 finished! INFO @ Mon, 29 Jun 2020 22:09:09: #2 predicted fragment length is 40 bps INFO @ Mon, 29 Jun 2020 22:09:09: #2 alternative fragment length(s) may be 40 bps INFO @ Mon, 29 Jun 2020 22:09:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.20_model.r WARNING @ Mon, 29 Jun 2020 22:09:09: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:09:09: #2 You may need to consider one of the other alternative d(s): 40 WARNING @ Mon, 29 Jun 2020 22:09:09: #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 22:09:09: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:09:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:09:16: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:09:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:09:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:09:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.10_summits.bed INFO @ Mon, 29 Jun 2020 22:09:34: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1628 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 29 Jun 2020 22:09:45: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:10:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:10:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:10:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1266821/ERX1266821.20_summits.bed INFO @ Mon, 29 Jun 2020 22:10:04: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1193 records, 4 fields): 2 millis CompletedMACS2peakCalling