Job ID = 6498027 SRX = SRX287900 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:16:32 prefetch.2.10.7: 1) Downloading 'SRR870089'... 2020-06-25T23:16:32 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:18:15 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:18:16 prefetch.2.10.7: 'SRR870089' is valid 2020-06-25T23:18:16 prefetch.2.10.7: 1) 'SRR870089' was downloaded successfully Read 13220574 spots for SRR870089/SRR870089.sra Written 13220574 spots for SRR870089/SRR870089.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: 00:06:02 13220574 reads; of these: 13220574 (100.00%) were unpaired; of these: 480117 (3.63%) aligned 0 times 9249202 (69.96%) aligned exactly 1 time 3491255 (26.41%) aligned >1 times 96.37% overall alignment rate Time searching: 00:06:02 Overall time: 00:06:02 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] 1100360 / 12740457 = 0.0864 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 @ Fri, 26 Jun 2020 08:29:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.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 @ Fri, 26 Jun 2020 08:29:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:29:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:29:27: 1000000 INFO @ Fri, 26 Jun 2020 08:29:34: 2000000 INFO @ Fri, 26 Jun 2020 08:29:41: 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 @ Fri, 26 Jun 2020 08:29:49: 4000000 INFO @ Fri, 26 Jun 2020 08:29:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.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 @ Fri, 26 Jun 2020 08:29:50: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:29:50: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:29:57: 5000000 INFO @ Fri, 26 Jun 2020 08:29:59: 1000000 INFO @ Fri, 26 Jun 2020 08:30:05: 6000000 INFO @ Fri, 26 Jun 2020 08:30:08: 2000000 INFO @ Fri, 26 Jun 2020 08:30:14: 7000000 BedGraph に変換中... INFO @ Fri, 26 Jun 2020 08:30:17: 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 @ Fri, 26 Jun 2020 08:30:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.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 @ Fri, 26 Jun 2020 08:30:20: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:30:20: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:30:22: 8000000 INFO @ Fri, 26 Jun 2020 08:30:27: 4000000 INFO @ Fri, 26 Jun 2020 08:30:29: 1000000 INFO @ Fri, 26 Jun 2020 08:30:31: 9000000 INFO @ Fri, 26 Jun 2020 08:30:37: 5000000 INFO @ Fri, 26 Jun 2020 08:30:39: 2000000 INFO @ Fri, 26 Jun 2020 08:30:40: 10000000 INFO @ Fri, 26 Jun 2020 08:30:46: 6000000 INFO @ Fri, 26 Jun 2020 08:30:49: 3000000 INFO @ Fri, 26 Jun 2020 08:30:49: 11000000 INFO @ Fri, 26 Jun 2020 08:30:55: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:30:55: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:30:55: #1 total tags in treatment: 11640097 INFO @ Fri, 26 Jun 2020 08:30:55: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:30:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:30:55: #1 tags after filtering in treatment: 11640097 INFO @ Fri, 26 Jun 2020 08:30:55: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:30:55: #1 finished! INFO @ Fri, 26 Jun 2020 08:30:55: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:30:55: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:30:55: 7000000 INFO @ Fri, 26 Jun 2020 08:30:56: #2 number of paired peaks: 259 WARNING @ Fri, 26 Jun 2020 08:30:56: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Fri, 26 Jun 2020 08:30:56: start model_add_line... INFO @ Fri, 26 Jun 2020 08:30:56: start X-correlation... INFO @ Fri, 26 Jun 2020 08:30:56: end of X-cor INFO @ Fri, 26 Jun 2020 08:30:56: #2 finished! INFO @ Fri, 26 Jun 2020 08:30:56: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 08:30:56: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 26 Jun 2020 08:30:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.05_model.r WARNING @ Fri, 26 Jun 2020 08:30:56: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:30:56: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 26 Jun 2020 08:30:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:30:56: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:30:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:30:58: 4000000 INFO @ Fri, 26 Jun 2020 08:31:05: 8000000 INFO @ Fri, 26 Jun 2020 08:31:08: 5000000 INFO @ Fri, 26 Jun 2020 08:31:14: 9000000 INFO @ Fri, 26 Jun 2020 08:31:18: 6000000 INFO @ Fri, 26 Jun 2020 08:31:22: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:31:23: 10000000 INFO @ Fri, 26 Jun 2020 08:31:27: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:31:32: 11000000 INFO @ Fri, 26 Jun 2020 08:31:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:31:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:31:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.05_summits.bed INFO @ Fri, 26 Jun 2020 08:31:35: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1918 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:31:36: 8000000 INFO @ Fri, 26 Jun 2020 08:31:38: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:31:38: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:31:38: #1 total tags in treatment: 11640097 INFO @ Fri, 26 Jun 2020 08:31:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:31:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:31:39: #1 tags after filtering in treatment: 11640097 INFO @ Fri, 26 Jun 2020 08:31:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:31:39: #1 finished! INFO @ Fri, 26 Jun 2020 08:31:39: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:31:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:31:40: #2 number of paired peaks: 259 WARNING @ Fri, 26 Jun 2020 08:31:40: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Fri, 26 Jun 2020 08:31:40: start model_add_line... INFO @ Fri, 26 Jun 2020 08:31:40: start X-correlation... INFO @ Fri, 26 Jun 2020 08:31:40: end of X-cor INFO @ Fri, 26 Jun 2020 08:31:40: #2 finished! INFO @ Fri, 26 Jun 2020 08:31:40: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 08:31:40: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 26 Jun 2020 08:31:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.10_model.r WARNING @ Fri, 26 Jun 2020 08:31:40: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:31:40: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 26 Jun 2020 08:31:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:31:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:31:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:31:46: 9000000 INFO @ Fri, 26 Jun 2020 08:31:54: 10000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:32:03: 11000000 INFO @ Fri, 26 Jun 2020 08:32:07: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:32:09: #1 tag size is determined as 50 bps INFO @ Fri, 26 Jun 2020 08:32:09: #1 tag size = 50 INFO @ Fri, 26 Jun 2020 08:32:09: #1 total tags in treatment: 11640097 INFO @ Fri, 26 Jun 2020 08:32:09: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:32:09: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 26 Jun 2020 08:32:09: #1 tags after filtering in treatment: 11640097 INFO @ Fri, 26 Jun 2020 08:32:09: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:32:09: #1 finished! INFO @ Fri, 26 Jun 2020 08:32:09: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:32:09: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:32:10: #2 number of paired peaks: 259 WARNING @ Fri, 26 Jun 2020 08:32:10: Fewer paired peaks (259) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 259 pairs to build model! INFO @ Fri, 26 Jun 2020 08:32:10: start model_add_line... INFO @ Fri, 26 Jun 2020 08:32:10: start X-correlation... INFO @ Fri, 26 Jun 2020 08:32:10: end of X-cor INFO @ Fri, 26 Jun 2020 08:32:10: #2 finished! INFO @ Fri, 26 Jun 2020 08:32:10: #2 predicted fragment length is 46 bps INFO @ Fri, 26 Jun 2020 08:32:10: #2 alternative fragment length(s) may be 46 bps INFO @ Fri, 26 Jun 2020 08:32:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.20_model.r WARNING @ Fri, 26 Jun 2020 08:32:10: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:32:10: #2 You may need to consider one of the other alternative d(s): 46 WARNING @ Fri, 26 Jun 2020 08:32:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 26 Jun 2020 08:32:10: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:32:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:32:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:32:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:32:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.10_summits.bed INFO @ Fri, 26 Jun 2020 08:32:21: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1352 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:32:37: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:32:51: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:32:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:32:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287900/SRX287900.20_summits.bed INFO @ Fri, 26 Jun 2020 08:32:51: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (959 records, 4 fields): 5 millis CompletedMACS2peakCalling