Job ID = 6527629 SRX = SRX1600224 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-29T13:05:36 prefetch.2.10.7: 1) Downloading 'SRR3187660'... 2020-06-29T13:05:36 prefetch.2.10.7: Downloading via HTTPS... 2020-06-29T13:05:56 prefetch.2.10.7: HTTPS download succeed 2020-06-29T13:05:56 prefetch.2.10.7: 'SRR3187660' is valid 2020-06-29T13:05:56 prefetch.2.10.7: 1) 'SRR3187660' was downloaded successfully Read 407897 spots for SRR3187660/SRR3187660.sra Written 407897 spots for SRR3187660/SRR3187660.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: 00:00:04 407897 reads; of these: 407897 (100.00%) were unpaired; of these: 321917 (78.92%) aligned 0 times 74864 (18.35%) aligned exactly 1 time 11116 (2.73%) aligned >1 times 21.08% overall alignment rate Time searching: 00:00:04 Overall time: 00:00:04 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] 30732 / 85980 = 0.3574 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 22:06:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.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 22:06:43: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:06:43: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:06:43: #1 tag size is determined as 76 bps INFO @ Mon, 29 Jun 2020 22:06:43: #1 tag size = 76 INFO @ Mon, 29 Jun 2020 22:06:43: #1 total tags in treatment: 55248 INFO @ Mon, 29 Jun 2020 22:06:43: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:06:43: #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 22:06:43: #1 tags after filtering in treatment: 55247 INFO @ Mon, 29 Jun 2020 22:06:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:06:43: #1 finished! INFO @ Mon, 29 Jun 2020 22:06:43: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:06:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:06:43: #2 number of paired peaks: 2498 INFO @ Mon, 29 Jun 2020 22:06:43: start model_add_line... INFO @ Mon, 29 Jun 2020 22:06:43: start X-correlation... INFO @ Mon, 29 Jun 2020 22:06:44: end of X-cor INFO @ Mon, 29 Jun 2020 22:06:44: #2 finished! INFO @ Mon, 29 Jun 2020 22:06:44: #2 predicted fragment length is 133 bps INFO @ Mon, 29 Jun 2020 22:06:44: #2 alternative fragment length(s) may be 133,221,295 bps INFO @ Mon, 29 Jun 2020 22:06:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.05_model.r WARNING @ Mon, 29 Jun 2020 22:06:44: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:06:44: #2 You may need to consider one of the other alternative d(s): 133,221,295 WARNING @ Mon, 29 Jun 2020 22:06:44: #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 22:06:44: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:06:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:06:44: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:06:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.05_peaks.xls INFO @ Mon, 29 Jun 2020 22:06:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.05_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:06:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.05_summits.bed INFO @ Mon, 29 Jun 2020 22:06:44: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (9 records, 4 fields): 1 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 @ Mon, 29 Jun 2020 22:07:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.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 22:07:13: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:07:13: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:07:13: #1 tag size is determined as 76 bps INFO @ Mon, 29 Jun 2020 22:07:13: #1 tag size = 76 INFO @ Mon, 29 Jun 2020 22:07:13: #1 total tags in treatment: 55248 INFO @ Mon, 29 Jun 2020 22:07:13: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:07:13: #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 22:07:13: #1 tags after filtering in treatment: 55247 INFO @ Mon, 29 Jun 2020 22:07:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:07:13: #1 finished! INFO @ Mon, 29 Jun 2020 22:07:13: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:07:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:07:13: #2 number of paired peaks: 2498 INFO @ Mon, 29 Jun 2020 22:07:13: start model_add_line... INFO @ Mon, 29 Jun 2020 22:07:13: start X-correlation... INFO @ Mon, 29 Jun 2020 22:07:13: end of X-cor INFO @ Mon, 29 Jun 2020 22:07:13: #2 finished! INFO @ Mon, 29 Jun 2020 22:07:13: #2 predicted fragment length is 133 bps INFO @ Mon, 29 Jun 2020 22:07:13: #2 alternative fragment length(s) may be 133,221,295 bps INFO @ Mon, 29 Jun 2020 22:07:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.10_model.r WARNING @ Mon, 29 Jun 2020 22:07:14: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:07:14: #2 You may need to consider one of the other alternative d(s): 133,221,295 WARNING @ Mon, 29 Jun 2020 22:07:14: #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 22:07:14: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:07:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:07:14: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:07:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.10_peaks.xls INFO @ Mon, 29 Jun 2020 22:07:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.10_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:07:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.10_summits.bed INFO @ Mon, 29 Jun 2020 22:07:14: Done! pass1 - making usageList (0 chroms): 0 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) 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 BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Mon, 29 Jun 2020 22:07:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.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 22:07:43: #1 read tag files... INFO @ Mon, 29 Jun 2020 22:07:43: #1 read treatment tags... INFO @ Mon, 29 Jun 2020 22:07:43: #1 tag size is determined as 76 bps INFO @ Mon, 29 Jun 2020 22:07:43: #1 tag size = 76 INFO @ Mon, 29 Jun 2020 22:07:43: #1 total tags in treatment: 55248 INFO @ Mon, 29 Jun 2020 22:07:43: #1 user defined the maximum tags... INFO @ Mon, 29 Jun 2020 22:07:43: #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 22:07:43: #1 tags after filtering in treatment: 55247 INFO @ Mon, 29 Jun 2020 22:07:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 29 Jun 2020 22:07:43: #1 finished! INFO @ Mon, 29 Jun 2020 22:07:43: #2 Build Peak Model... INFO @ Mon, 29 Jun 2020 22:07:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 29 Jun 2020 22:07:44: #2 number of paired peaks: 2498 INFO @ Mon, 29 Jun 2020 22:07:44: start model_add_line... INFO @ Mon, 29 Jun 2020 22:07:44: start X-correlation... INFO @ Mon, 29 Jun 2020 22:07:44: end of X-cor INFO @ Mon, 29 Jun 2020 22:07:44: #2 finished! INFO @ Mon, 29 Jun 2020 22:07:44: #2 predicted fragment length is 133 bps INFO @ Mon, 29 Jun 2020 22:07:44: #2 alternative fragment length(s) may be 133,221,295 bps INFO @ Mon, 29 Jun 2020 22:07:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.20_model.r WARNING @ Mon, 29 Jun 2020 22:07:44: #2 Since the d (133) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 29 Jun 2020 22:07:44: #2 You may need to consider one of the other alternative d(s): 133,221,295 WARNING @ Mon, 29 Jun 2020 22:07:44: #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 22:07:44: #3 Call peaks... INFO @ Mon, 29 Jun 2020 22:07:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 29 Jun 2020 22:07:44: #3 Call peaks for each chromosome... INFO @ Mon, 29 Jun 2020 22:07:44: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.20_peaks.xls INFO @ Mon, 29 Jun 2020 22:07:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.20_peaks.narrowPeak INFO @ Mon, 29 Jun 2020 22:07:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1600224/SRX1600224.20_summits.bed INFO @ Mon, 29 Jun 2020 22:07:44: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling