Job ID = 6498745 SRX = SRX750068 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:57:34 prefetch.2.10.7: 1) Downloading 'SRR1638749'... 2020-06-25T23:57:34 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:00:34 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:00:34 prefetch.2.10.7: 1) 'SRR1638749' was downloaded successfully Read 23683577 spots for SRR1638749/SRR1638749.sra Written 23683577 spots for SRR1638749/SRR1638749.sra 2020-06-26T00:02:02 prefetch.2.10.7: 1) Downloading 'SRR1638750'... 2020-06-26T00:02:02 prefetch.2.10.7: Downloading via HTTPS... 2020-06-26T00:04:29 prefetch.2.10.7: HTTPS download succeed 2020-06-26T00:04:29 prefetch.2.10.7: 1) 'SRR1638750' was downloaded successfully Read 20374466 spots for SRR1638750/SRR1638750.sra Written 20374466 spots for SRR1638750/SRR1638750.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: 00:16:23 44058043 reads; of these: 44058043 (100.00%) were unpaired; of these: 9369586 (21.27%) aligned 0 times 24729108 (56.13%) aligned exactly 1 time 9959349 (22.61%) aligned >1 times 78.73% overall alignment rate Time searching: 00:16:23 Overall time: 00:16:23 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 16 files... [bam_rmdupse_core] 32406160 / 34688457 = 0.9342 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 09:28:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.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 09:28:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:28:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:28:32: 1000000 INFO @ Fri, 26 Jun 2020 09:28:39: 2000000 INFO @ Fri, 26 Jun 2020 09:28:40: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 09:28:40: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 09:28:40: #1 total tags in treatment: 2282297 INFO @ Fri, 26 Jun 2020 09:28:40: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:28:40: #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 09:28:40: #1 tags after filtering in treatment: 2282297 INFO @ Fri, 26 Jun 2020 09:28:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:28:40: #1 finished! INFO @ Fri, 26 Jun 2020 09:28:40: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:28:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:28:41: #2 number of paired peaks: 3424 INFO @ Fri, 26 Jun 2020 09:28:41: start model_add_line... INFO @ Fri, 26 Jun 2020 09:28:41: start X-correlation... INFO @ Fri, 26 Jun 2020 09:28:41: end of X-cor INFO @ Fri, 26 Jun 2020 09:28:41: #2 finished! INFO @ Fri, 26 Jun 2020 09:28:41: #2 predicted fragment length is 78 bps INFO @ Fri, 26 Jun 2020 09:28:41: #2 alternative fragment length(s) may be 78 bps INFO @ Fri, 26 Jun 2020 09:28:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.05_model.r WARNING @ Fri, 26 Jun 2020 09:28:41: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:28:41: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Fri, 26 Jun 2020 09:28:41: #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 09:28:41: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:28:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:28:46: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:28:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.05_peaks.xls INFO @ Fri, 26 Jun 2020 09:28:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:28:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.05_summits.bed INFO @ Fri, 26 Jun 2020 09:28:48: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3581 records, 4 fields): 5 millis CompletedMACS2peakCalling 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 09:28:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.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 09:28:55: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:28:55: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:29:01: 1000000 INFO @ Fri, 26 Jun 2020 09:29:06: 2000000 INFO @ Fri, 26 Jun 2020 09:29:08: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 09:29:08: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 09:29:08: #1 total tags in treatment: 2282297 INFO @ Fri, 26 Jun 2020 09:29:08: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:29:08: #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 09:29:08: #1 tags after filtering in treatment: 2282297 INFO @ Fri, 26 Jun 2020 09:29:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:29:08: #1 finished! INFO @ Fri, 26 Jun 2020 09:29:08: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:29:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:29:08: #2 number of paired peaks: 3424 INFO @ Fri, 26 Jun 2020 09:29:08: start model_add_line... INFO @ Fri, 26 Jun 2020 09:29:08: start X-correlation... INFO @ Fri, 26 Jun 2020 09:29:08: end of X-cor INFO @ Fri, 26 Jun 2020 09:29:08: #2 finished! INFO @ Fri, 26 Jun 2020 09:29:08: #2 predicted fragment length is 78 bps INFO @ Fri, 26 Jun 2020 09:29:08: #2 alternative fragment length(s) may be 78 bps INFO @ Fri, 26 Jun 2020 09:29:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.10_model.r WARNING @ Fri, 26 Jun 2020 09:29:08: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:29:08: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Fri, 26 Jun 2020 09:29:08: #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 09:29:08: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:29:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:29:14: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:29:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.10_peaks.xls INFO @ Fri, 26 Jun 2020 09:29:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:29:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.10_summits.bed INFO @ Fri, 26 Jun 2020 09:29:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2153 records, 4 fields): 4 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 @ Fri, 26 Jun 2020 09:29:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.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 09:29:25: #1 read tag files... INFO @ Fri, 26 Jun 2020 09:29:25: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 09:29:31: 1000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 09:29:37: 2000000 BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 09:29:38: #1 tag size is determined as 67 bps INFO @ Fri, 26 Jun 2020 09:29:38: #1 tag size = 67 INFO @ Fri, 26 Jun 2020 09:29:38: #1 total tags in treatment: 2282297 INFO @ Fri, 26 Jun 2020 09:29:38: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 09:29:38: #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 09:29:38: #1 tags after filtering in treatment: 2282297 INFO @ Fri, 26 Jun 2020 09:29:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 09:29:38: #1 finished! INFO @ Fri, 26 Jun 2020 09:29:38: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 09:29:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 09:29:39: #2 number of paired peaks: 3424 INFO @ Fri, 26 Jun 2020 09:29:39: start model_add_line... INFO @ Fri, 26 Jun 2020 09:29:39: start X-correlation... INFO @ Fri, 26 Jun 2020 09:29:39: end of X-cor INFO @ Fri, 26 Jun 2020 09:29:39: #2 finished! INFO @ Fri, 26 Jun 2020 09:29:39: #2 predicted fragment length is 78 bps INFO @ Fri, 26 Jun 2020 09:29:39: #2 alternative fragment length(s) may be 78 bps INFO @ Fri, 26 Jun 2020 09:29:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.20_model.r WARNING @ Fri, 26 Jun 2020 09:29:39: #2 Since the d (78) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 09:29:39: #2 You may need to consider one of the other alternative d(s): 78 WARNING @ Fri, 26 Jun 2020 09:29:39: #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 09:29:39: #3 Call peaks... INFO @ Fri, 26 Jun 2020 09:29:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 09:29:44: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 09:29:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.20_peaks.xls INFO @ Fri, 26 Jun 2020 09:29:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 09:29:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX750068/SRX750068.20_summits.bed INFO @ Fri, 26 Jun 2020 09:29:46: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1334 records, 4 fields): 3 millis CompletedMACS2peakCalling