Job ID = 6527819 SRX = SRX287749 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:28:07 prefetch.2.10.7: 1) Downloading 'SRR869938'... 2020-06-29T13:28:07 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:30:48 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:30:48 prefetch.2.10.7: 1) 'SRR869938' was downloaded successfully Read 19172821 spots for SRR869938/SRR869938.sra Written 19172821 spots for SRR869938/SRR869938.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: 00:07:38 19172821 reads; of these: 19172821 (100.00%) were unpaired; of these: 728072 (3.80%) aligned 0 times 12514313 (65.27%) aligned exactly 1 time 5930436 (30.93%) aligned >1 times 96.20% overall alignment rate Time searching: 00:07:38 Overall time: 00:07:38 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] 2854536 / 18444749 = 0.1548 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 22:48:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.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 22:48:16: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:48:16: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:48:21: 1000000 INFO @ Mon, 29 Jun 2020 22:48:26: 2000000 INFO @ Mon, 29 Jun 2020 22:48:31: 3000000 INFO @ Mon, 29 Jun 2020 22:48:36: 4000000 INFO @ Mon, 29 Jun 2020 22:48:41: 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 22:48:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.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 22:48:46: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:48:46: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:48:46: 6000000 INFO @ Mon, 29 Jun 2020 22:48:51: 1000000 INFO @ Mon, 29 Jun 2020 22:48:51: 7000000 INFO @ Mon, 29 Jun 2020 22:48:56: 2000000 INFO @ Mon, 29 Jun 2020 22:48:56: 8000000 INFO @ Mon, 29 Jun 2020 22:49:01: 3000000 INFO @ Mon, 29 Jun 2020 22:49:01: 9000000 INFO @ Mon, 29 Jun 2020 22:49:06: 4000000 INFO @ Mon, 29 Jun 2020 22:49:06: 10000000 INFO @ Mon, 29 Jun 2020 22:49:12: 5000000 INFO @ Mon, 29 Jun 2020 22:49:12: 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 22:49:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.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 22:49:16: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:49:16: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:49:17: 12000000 INFO @ Mon, 29 Jun 2020 22:49:17: 6000000 INFO @ Mon, 29 Jun 2020 22:49:21: 1000000 INFO @ Mon, 29 Jun 2020 22:49:22: 13000000 INFO @ Mon, 29 Jun 2020 22:49:22: 7000000 INFO @ Mon, 29 Jun 2020 22:49:27: 2000000 INFO @ Mon, 29 Jun 2020 22:49:28: 14000000 INFO @ Mon, 29 Jun 2020 22:49:28: 8000000 INFO @ Mon, 29 Jun 2020 22:49:32: 3000000 INFO @ Mon, 29 Jun 2020 22:49:33: 15000000 INFO @ Mon, 29 Jun 2020 22:49:33: 9000000 INFO @ Mon, 29 Jun 2020 22:49:37: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:49:37: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:49:37: #1 total tags in treatment: 15590213 INFO @ Mon, 29 Jun 2020 22:49:37: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:49:37: #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 22:49:37: #1 tags after filtering in treatment: 15590213 INFO @ Mon, 29 Jun 2020 22:49:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:49:37: #1 finished! INFO @ Mon, 29 Jun 2020 22:49:37: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:49:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:49:38: 4000000 INFO @ Mon, 29 Jun 2020 22:49:38: #2 number of paired peaks: 247 WARNING @ Mon, 29 Jun 2020 22:49:38: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Mon, 29 Jun 2020 22:49:38: start model_add_line... INFO @ Mon, 29 Jun 2020 22:49:38: start X-correlation... INFO @ Mon, 29 Jun 2020 22:49:38: end of X-cor INFO @ Mon, 29 Jun 2020 22:49:38: #2 finished! INFO @ Mon, 29 Jun 2020 22:49:38: #2 predicted fragment length is 45 bps INFO @ Mon, 29 Jun 2020 22:49:38: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 29 Jun 2020 22:49:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.05_model.r WARNING @ Mon, 29 Jun 2020 22:49:38: #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 22:49:38: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 29 Jun 2020 22:49:38: #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 22:49:38: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:49:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:49:39: 10000000 INFO @ Mon, 29 Jun 2020 22:49:43: 5000000 INFO @ Mon, 29 Jun 2020 22:49:45: 11000000 INFO @ Mon, 29 Jun 2020 22:49:49: 6000000 INFO @ Mon, 29 Jun 2020 22:49:50: 12000000 INFO @ Mon, 29 Jun 2020 22:49:54: 7000000 INFO @ Mon, 29 Jun 2020 22:49:55: 13000000 INFO @ Mon, 29 Jun 2020 22:49:59: 8000000 INFO @ Mon, 29 Jun 2020 22:50:01: 14000000 INFO @ Mon, 29 Jun 2020 22:50:05: 9000000 INFO @ Mon, 29 Jun 2020 22:50:06: 15000000 INFO @ Mon, 29 Jun 2020 22:50:07: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:50:09: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:50:09: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:50:09: #1 total tags in treatment: 15590213 INFO @ Mon, 29 Jun 2020 22:50:09: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:50:09: #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 22:50:10: #1 tags after filtering in treatment: 15590213 INFO @ Mon, 29 Jun 2020 22:50:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:50:10: #1 finished! INFO @ Mon, 29 Jun 2020 22:50:10: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:50:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:50:10: 10000000 INFO @ Mon, 29 Jun 2020 22:50:11: #2 number of paired peaks: 247 WARNING @ Mon, 29 Jun 2020 22:50:11: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Mon, 29 Jun 2020 22:50:11: start model_add_line... INFO @ Mon, 29 Jun 2020 22:50:11: start X-correlation... INFO @ Mon, 29 Jun 2020 22:50:11: end of X-cor INFO @ Mon, 29 Jun 2020 22:50:11: #2 finished! INFO @ Mon, 29 Jun 2020 22:50:11: #2 predicted fragment length is 45 bps INFO @ Mon, 29 Jun 2020 22:50:11: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 29 Jun 2020 22:50:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.10_model.r WARNING @ Mon, 29 Jun 2020 22:50:11: #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 22:50:11: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 29 Jun 2020 22:50:11: #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 22:50:11: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:50:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:50:15: 11000000 INFO @ Mon, 29 Jun 2020 22:50:21: 12000000 INFO @ Mon, 29 Jun 2020 22:50:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:50:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:50:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.05_summits.bed INFO @ Mon, 29 Jun 2020 22:50:21: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1994 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 29 Jun 2020 22:50:26: 13000000 INFO @ Mon, 29 Jun 2020 22:50:30: 14000000 INFO @ Mon, 29 Jun 2020 22:50:35: 15000000 INFO @ Mon, 29 Jun 2020 22:50:39: #1 tag size is determined as 50 bps INFO @ Mon, 29 Jun 2020 22:50:39: #1 tag size = 50 INFO @ Mon, 29 Jun 2020 22:50:39: #1 total tags in treatment: 15590213 INFO @ Mon, 29 Jun 2020 22:50:39: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:50:39: #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 22:50:39: #1 tags after filtering in treatment: 15590213 INFO @ Mon, 29 Jun 2020 22:50:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:50:39: #1 finished! INFO @ Mon, 29 Jun 2020 22:50:39: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:50:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:50:40: #2 number of paired peaks: 247 WARNING @ Mon, 29 Jun 2020 22:50:40: Fewer paired peaks (247) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 247 pairs to build model! INFO @ Mon, 29 Jun 2020 22:50:40: start model_add_line... INFO @ Mon, 29 Jun 2020 22:50:40: start X-correlation... INFO @ Mon, 29 Jun 2020 22:50:40: end of X-cor INFO @ Mon, 29 Jun 2020 22:50:40: #2 finished! INFO @ Mon, 29 Jun 2020 22:50:40: #2 predicted fragment length is 45 bps INFO @ Mon, 29 Jun 2020 22:50:40: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 29 Jun 2020 22:50:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.20_model.r WARNING @ Mon, 29 Jun 2020 22:50:40: #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 22:50:40: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 29 Jun 2020 22:50:40: #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 22:50:40: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:50:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:50:40: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:50:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:50:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:50:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.10_summits.bed INFO @ Mon, 29 Jun 2020 22:50:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1631 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:51:09: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:51:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:51:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:51:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287749/SRX287749.20_summits.bed INFO @ Mon, 29 Jun 2020 22:51:23: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (1265 records, 4 fields): 3 millis CompletedMACS2peakCalling