Job ID = 6456250 SRX = SRX331403 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T10:41:23 prefetch.2.10.7: 1) Downloading 'SRR947640'... 2020-06-21T10:41:23 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T10:43:55 prefetch.2.10.7: HTTPS download succeed 2020-06-21T10:43:56 prefetch.2.10.7: 'SRR947640' is valid 2020-06-21T10:43:56 prefetch.2.10.7: 1) 'SRR947640' was downloaded successfully Read 11861028 spots for SRR947640/SRR947640.sra Written 11861028 spots for SRR947640/SRR947640.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: 00:03:02 11861028 reads; of these: 11861028 (100.00%) were unpaired; of these: 1507645 (12.71%) aligned 0 times 6957557 (58.66%) aligned exactly 1 time 3395826 (28.63%) aligned >1 times 87.29% overall alignment rate Time searching: 00:03:02 Overall time: 00:03:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 1870 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 4019053 / 10353383 = 0.3882 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 @ Sun, 21 Jun 2020 19:50:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.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 @ Sun, 21 Jun 2020 19:50:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:50:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:50:25: 1000000 INFO @ Sun, 21 Jun 2020 19:50:30: 2000000 INFO @ Sun, 21 Jun 2020 19:50:36: 3000000 INFO @ Sun, 21 Jun 2020 19:50:41: 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 @ Sun, 21 Jun 2020 19:50:48: 5000000 INFO @ Sun, 21 Jun 2020 19:50:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.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 @ Sun, 21 Jun 2020 19:50:49: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:50:49: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:50:54: 6000000 INFO @ Sun, 21 Jun 2020 19:50:55: 1000000 INFO @ Sun, 21 Jun 2020 19:50:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:50:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:50:56: #1 total tags in treatment: 6334330 INFO @ Sun, 21 Jun 2020 19:50:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:50:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:50:56: #1 tags after filtering in treatment: 6334316 INFO @ Sun, 21 Jun 2020 19:50:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:50:56: #1 finished! INFO @ Sun, 21 Jun 2020 19:50:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:50:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:50:56: #2 number of paired peaks: 1069 INFO @ Sun, 21 Jun 2020 19:50:56: start model_add_line... INFO @ Sun, 21 Jun 2020 19:50:57: start X-correlation... INFO @ Sun, 21 Jun 2020 19:50:57: end of X-cor INFO @ Sun, 21 Jun 2020 19:50:57: #2 finished! INFO @ Sun, 21 Jun 2020 19:50:57: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 19:50:57: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sun, 21 Jun 2020 19:50:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.05_model.r WARNING @ Sun, 21 Jun 2020 19:50:57: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:50:57: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sun, 21 Jun 2020 19:50:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:50:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:50:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:51:01: 2000000 INFO @ Sun, 21 Jun 2020 19:51:06: 3000000 INFO @ Sun, 21 Jun 2020 19:51:10: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:51:12: 4000000 INFO @ Sun, 21 Jun 2020 19:51:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.05_summits.bed INFO @ Sun, 21 Jun 2020 19:51:16: Done! pass1 - making usageList (642 chroms): 1 millis pass2 - checking and writing primary data (2137 records, 4 fields): 19 millis CompletedMACS2peakCalling 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 @ Sun, 21 Jun 2020 19:51:18: 5000000 INFO @ Sun, 21 Jun 2020 19:51:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.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 @ Sun, 21 Jun 2020 19:51:19: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:51:19: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:51:25: 6000000 INFO @ Sun, 21 Jun 2020 19:51:26: 1000000 INFO @ Sun, 21 Jun 2020 19:51:27: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:51:27: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:51:27: #1 total tags in treatment: 6334330 INFO @ Sun, 21 Jun 2020 19:51:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:51:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:51:27: #1 tags after filtering in treatment: 6334316 INFO @ Sun, 21 Jun 2020 19:51:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:51:27: #1 finished! INFO @ Sun, 21 Jun 2020 19:51:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:51:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:51:28: #2 number of paired peaks: 1069 INFO @ Sun, 21 Jun 2020 19:51:28: start model_add_line... INFO @ Sun, 21 Jun 2020 19:51:28: start X-correlation... INFO @ Sun, 21 Jun 2020 19:51:28: end of X-cor INFO @ Sun, 21 Jun 2020 19:51:28: #2 finished! INFO @ Sun, 21 Jun 2020 19:51:28: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 19:51:28: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sun, 21 Jun 2020 19:51:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.10_model.r WARNING @ Sun, 21 Jun 2020 19:51:28: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:51:28: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sun, 21 Jun 2020 19:51:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:51:28: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:51:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:51:32: 2000000 INFO @ Sun, 21 Jun 2020 19:51:38: 3000000 INFO @ Sun, 21 Jun 2020 19:51:42: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:51:44: 4000000 INFO @ Sun, 21 Jun 2020 19:51:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:51:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:51:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.10_summits.bed INFO @ Sun, 21 Jun 2020 19:51:48: Done! pass1 - making usageList (364 chroms): 1 millis pass2 - checking and writing primary data (972 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:51:50: 5000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:51:56: 6000000 INFO @ Sun, 21 Jun 2020 19:51:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 19:51:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 19:51:58: #1 total tags in treatment: 6334330 INFO @ Sun, 21 Jun 2020 19:51:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:51:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 21 Jun 2020 19:51:58: #1 tags after filtering in treatment: 6334316 INFO @ Sun, 21 Jun 2020 19:51:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:51:58: #1 finished! INFO @ Sun, 21 Jun 2020 19:51:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:51:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:51:59: #2 number of paired peaks: 1069 INFO @ Sun, 21 Jun 2020 19:51:59: start model_add_line... INFO @ Sun, 21 Jun 2020 19:51:59: start X-correlation... INFO @ Sun, 21 Jun 2020 19:51:59: end of X-cor INFO @ Sun, 21 Jun 2020 19:51:59: #2 finished! INFO @ Sun, 21 Jun 2020 19:51:59: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 19:51:59: #2 alternative fragment length(s) may be 4,60 bps INFO @ Sun, 21 Jun 2020 19:51:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.20_model.r WARNING @ Sun, 21 Jun 2020 19:51:59: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:51:59: #2 You may need to consider one of the other alternative d(s): 4,60 WARNING @ Sun, 21 Jun 2020 19:51:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 21 Jun 2020 19:51:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:51:59: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:52:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:52:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:52:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:52:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX331403/SRX331403.20_summits.bed INFO @ Sun, 21 Jun 2020 19:52:19: Done! pass1 - making usageList (196 chroms): 1 millis pass2 - checking and writing primary data (418 records, 4 fields): 7 millis CompletedMACS2peakCalling