Job ID = 6498702 SRX = SRX706815 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:40:00 prefetch.2.10.7: 1) Downloading 'SRR1581496'... 2020-06-25T23:40:00 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:42:47 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:42:47 prefetch.2.10.7: 1) 'SRR1581496' was downloaded successfully Read 28322420 spots for SRR1581496/SRR1581496.sra Written 28322420 spots for SRR1581496/SRR1581496.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: 00:04:33 28322420 reads; of these: 28322420 (100.00%) were unpaired; of these: 14831171 (52.37%) aligned 0 times 11199169 (39.54%) aligned exactly 1 time 2292080 (8.09%) aligned >1 times 47.63% overall alignment rate Time searching: 00:04:33 Overall time: 00:04:33 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] 8642888 / 13491249 = 0.6406 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 08:51:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.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 08:51:11: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:51:11: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:51:17: 1000000 INFO @ Fri, 26 Jun 2020 08:51:23: 2000000 INFO @ Fri, 26 Jun 2020 08:51:29: 3000000 INFO @ Fri, 26 Jun 2020 08:51:35: 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 @ Fri, 26 Jun 2020 08:51:40: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 08:51:40: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 08:51:40: #1 total tags in treatment: 4848361 INFO @ Fri, 26 Jun 2020 08:51:40: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:51:40: #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 08:51:40: #1 tags after filtering in treatment: 4848361 INFO @ Fri, 26 Jun 2020 08:51:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:51:40: #1 finished! INFO @ Fri, 26 Jun 2020 08:51:40: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:51:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:51:40: #2 number of paired peaks: 690 WARNING @ Fri, 26 Jun 2020 08:51:40: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Fri, 26 Jun 2020 08:51:40: start model_add_line... INFO @ Fri, 26 Jun 2020 08:51:40: start X-correlation... INFO @ Fri, 26 Jun 2020 08:51:40: end of X-cor INFO @ Fri, 26 Jun 2020 08:51:40: #2 finished! INFO @ Fri, 26 Jun 2020 08:51:40: #2 predicted fragment length is 88 bps INFO @ Fri, 26 Jun 2020 08:51:40: #2 alternative fragment length(s) may be 4,58,65,88,104,557 bps INFO @ Fri, 26 Jun 2020 08:51:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.05_model.r WARNING @ Fri, 26 Jun 2020 08:51:40: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:51:40: #2 You may need to consider one of the other alternative d(s): 4,58,65,88,104,557 WARNING @ Fri, 26 Jun 2020 08:51:40: #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 08:51:40: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:51:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:51:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.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 08:51:41: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:51:41: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:51:46: 1000000 INFO @ Fri, 26 Jun 2020 08:51:51: 2000000 INFO @ Fri, 26 Jun 2020 08:51:51: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:51:56: 3000000 INFO @ Fri, 26 Jun 2020 08:51:57: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:51:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:51:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.05_summits.bed INFO @ Fri, 26 Jun 2020 08:51:57: Done! INFO @ Fri, 26 Jun 2020 08:52:01: 4000000 INFO @ Fri, 26 Jun 2020 08:52:05: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 08:52:05: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 08:52:05: #1 total tags in treatment: 4848361 INFO @ Fri, 26 Jun 2020 08:52:05: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:52:05: #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 08:52:05: #1 tags after filtering in treatment: 4848361 INFO @ Fri, 26 Jun 2020 08:52:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:52:05: #1 finished! INFO @ Fri, 26 Jun 2020 08:52:05: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:52:05: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (849 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:52:05: #2 number of paired peaks: 690 WARNING @ Fri, 26 Jun 2020 08:52:05: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Fri, 26 Jun 2020 08:52:05: start model_add_line... INFO @ Fri, 26 Jun 2020 08:52:05: start X-correlation... INFO @ Fri, 26 Jun 2020 08:52:05: end of X-cor INFO @ Fri, 26 Jun 2020 08:52:05: #2 finished! INFO @ Fri, 26 Jun 2020 08:52:05: #2 predicted fragment length is 88 bps INFO @ Fri, 26 Jun 2020 08:52:05: #2 alternative fragment length(s) may be 4,58,65,88,104,557 bps INFO @ Fri, 26 Jun 2020 08:52:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.10_model.r WARNING @ Fri, 26 Jun 2020 08:52:05: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:52:05: #2 You may need to consider one of the other alternative d(s): 4,58,65,88,104,557 WARNING @ Fri, 26 Jun 2020 08:52:05: #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 08:52:05: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:52:05: #3 Pre-compute pvalue-qvalue table... 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 @ Fri, 26 Jun 2020 08:52:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.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 08:52:11: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:52:11: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:52:16: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:52:18: 1000000 INFO @ Fri, 26 Jun 2020 08:52:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:52:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:52:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.10_summits.bed INFO @ Fri, 26 Jun 2020 08:52:21: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (361 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:52:23: 2000000 INFO @ Fri, 26 Jun 2020 08:52:28: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:52:33: 4000000 INFO @ Fri, 26 Jun 2020 08:52:37: #1 tag size is determined as 44 bps INFO @ Fri, 26 Jun 2020 08:52:37: #1 tag size = 44 INFO @ Fri, 26 Jun 2020 08:52:37: #1 total tags in treatment: 4848361 INFO @ Fri, 26 Jun 2020 08:52:37: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:52:37: #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 08:52:37: #1 tags after filtering in treatment: 4848361 INFO @ Fri, 26 Jun 2020 08:52:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:52:37: #1 finished! INFO @ Fri, 26 Jun 2020 08:52:37: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:52:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:52:38: #2 number of paired peaks: 690 WARNING @ Fri, 26 Jun 2020 08:52:38: Fewer paired peaks (690) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 690 pairs to build model! INFO @ Fri, 26 Jun 2020 08:52:38: start model_add_line... INFO @ Fri, 26 Jun 2020 08:52:38: start X-correlation... INFO @ Fri, 26 Jun 2020 08:52:38: end of X-cor INFO @ Fri, 26 Jun 2020 08:52:38: #2 finished! INFO @ Fri, 26 Jun 2020 08:52:38: #2 predicted fragment length is 88 bps INFO @ Fri, 26 Jun 2020 08:52:38: #2 alternative fragment length(s) may be 4,58,65,88,104,557 bps INFO @ Fri, 26 Jun 2020 08:52:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.20_model.r WARNING @ Fri, 26 Jun 2020 08:52:38: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:52:38: #2 You may need to consider one of the other alternative d(s): 4,58,65,88,104,557 WARNING @ Fri, 26 Jun 2020 08:52:38: #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 08:52:38: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:52:38: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:52:48: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:52:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:52:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:52:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX706815/SRX706815.20_summits.bed INFO @ Fri, 26 Jun 2020 08:52:53: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (116 records, 4 fields): 1 millis CompletedMACS2peakCalling