Job ID = 6457551 SRX = SRX4669040 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:51:03 prefetch.2.10.7: 1) Downloading 'SRR7817565'... 2020-06-21T11:51:03 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:52:17 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:52:17 prefetch.2.10.7: 'SRR7817565' is valid 2020-06-21T11:52:17 prefetch.2.10.7: 1) 'SRR7817565' was downloaded successfully 2020-06-21T11:52:17 prefetch.2.10.7: 'SRR7817565' has 0 unresolved dependencies Read 9005462 spots for SRR7817565/SRR7817565.sra Written 9005462 spots for SRR7817565/SRR7817565.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: 00:02:29 9005462 reads; of these: 9005462 (100.00%) were unpaired; of these: 323001 (3.59%) aligned 0 times 5731727 (63.65%) aligned exactly 1 time 2950734 (32.77%) aligned >1 times 96.41% overall alignment rate Time searching: 00:02:29 Overall time: 00:02:29 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_rmdupse_core] 1491422 / 8682461 = 0.1718 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 20:57:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.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 20:57:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:57:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:57:22: 1000000 INFO @ Sun, 21 Jun 2020 20:57:27: 2000000 INFO @ Sun, 21 Jun 2020 20:57:32: 3000000 INFO @ Sun, 21 Jun 2020 20:57:38: 4000000 INFO @ Sun, 21 Jun 2020 20:57:43: 5000000 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 20:57:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.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 20:57:47: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:57:47: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:57:48: 6000000 INFO @ Sun, 21 Jun 2020 20:57:52: 1000000 INFO @ Sun, 21 Jun 2020 20:57:54: 7000000 INFO @ Sun, 21 Jun 2020 20:57:55: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:57:55: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:57:55: #1 total tags in treatment: 7191039 INFO @ Sun, 21 Jun 2020 20:57:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:57:55: #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 20:57:55: #1 tags after filtering in treatment: 7191001 INFO @ Sun, 21 Jun 2020 20:57:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:57:55: #1 finished! INFO @ Sun, 21 Jun 2020 20:57:55: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:57:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:57:56: #2 number of paired peaks: 1301 INFO @ Sun, 21 Jun 2020 20:57:56: start model_add_line... INFO @ Sun, 21 Jun 2020 20:57:56: start X-correlation... INFO @ Sun, 21 Jun 2020 20:57:56: end of X-cor INFO @ Sun, 21 Jun 2020 20:57:56: #2 finished! INFO @ Sun, 21 Jun 2020 20:57:56: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 20:57:56: #2 alternative fragment length(s) may be 4,96 bps INFO @ Sun, 21 Jun 2020 20:57:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.05_model.r WARNING @ Sun, 21 Jun 2020 20:57:56: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:57:56: #2 You may need to consider one of the other alternative d(s): 4,96 WARNING @ Sun, 21 Jun 2020 20:57:56: #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 20:57:56: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:57:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:57:56: 2000000 INFO @ Sun, 21 Jun 2020 20:58:01: 3000000 INFO @ Sun, 21 Jun 2020 20:58:05: 4000000 INFO @ Sun, 21 Jun 2020 20:58:10: 5000000 INFO @ Sun, 21 Jun 2020 20:58:13: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:58:15: 6000000 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 20:58:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.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 20:58:17: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:58:17: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:58:20: 7000000 INFO @ Sun, 21 Jun 2020 20:58:21: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:58:21: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:58:21: #1 total tags in treatment: 7191039 INFO @ Sun, 21 Jun 2020 20:58:21: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:58:21: #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 20:58:21: #1 tags after filtering in treatment: 7191001 INFO @ Sun, 21 Jun 2020 20:58:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:58:21: #1 finished! INFO @ Sun, 21 Jun 2020 20:58:21: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:58:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:58:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:58:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:58:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.05_summits.bed INFO @ Sun, 21 Jun 2020 20:58:21: Done! pass1 - making usageList (392 chroms): 1 millis pass2 - checking and writing primary data (2779 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:58:22: #2 number of paired peaks: 1301 INFO @ Sun, 21 Jun 2020 20:58:22: start model_add_line... INFO @ Sun, 21 Jun 2020 20:58:22: start X-correlation... INFO @ Sun, 21 Jun 2020 20:58:22: end of X-cor INFO @ Sun, 21 Jun 2020 20:58:22: #2 finished! INFO @ Sun, 21 Jun 2020 20:58:22: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 20:58:22: #2 alternative fragment length(s) may be 4,96 bps INFO @ Sun, 21 Jun 2020 20:58:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.10_model.r WARNING @ Sun, 21 Jun 2020 20:58:22: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:58:22: #2 You may need to consider one of the other alternative d(s): 4,96 WARNING @ Sun, 21 Jun 2020 20:58:22: #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 20:58:22: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:58:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:58:22: 1000000 INFO @ Sun, 21 Jun 2020 20:58:26: 2000000 INFO @ Sun, 21 Jun 2020 20:58:31: 3000000 INFO @ Sun, 21 Jun 2020 20:58:35: 4000000 INFO @ Sun, 21 Jun 2020 20:58:38: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:58:40: 5000000 INFO @ Sun, 21 Jun 2020 20:58:45: 6000000 INFO @ Sun, 21 Jun 2020 20:58:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:58:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:58:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.10_summits.bed INFO @ Sun, 21 Jun 2020 20:58:46: Done! pass1 - making usageList (259 chroms): 1 millis pass2 - checking and writing primary data (939 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:58:50: 7000000 INFO @ Sun, 21 Jun 2020 20:58:51: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 20:58:51: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 20:58:51: #1 total tags in treatment: 7191039 INFO @ Sun, 21 Jun 2020 20:58:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:58:51: #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 20:58:51: #1 tags after filtering in treatment: 7191001 INFO @ Sun, 21 Jun 2020 20:58:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:58:51: #1 finished! INFO @ Sun, 21 Jun 2020 20:58:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:58:51: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:58:52: #2 number of paired peaks: 1301 INFO @ Sun, 21 Jun 2020 20:58:52: start model_add_line... INFO @ Sun, 21 Jun 2020 20:58:52: start X-correlation... INFO @ Sun, 21 Jun 2020 20:58:52: end of X-cor INFO @ Sun, 21 Jun 2020 20:58:52: #2 finished! INFO @ Sun, 21 Jun 2020 20:58:52: #2 predicted fragment length is 96 bps INFO @ Sun, 21 Jun 2020 20:58:52: #2 alternative fragment length(s) may be 4,96 bps INFO @ Sun, 21 Jun 2020 20:58:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.20_model.r WARNING @ Sun, 21 Jun 2020 20:58:52: #2 Since the d (96) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:58:52: #2 You may need to consider one of the other alternative d(s): 4,96 WARNING @ Sun, 21 Jun 2020 20:58:52: #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 20:58:52: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:58:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:59:07: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:59:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:59:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:59:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4669040/SRX4669040.20_summits.bed INFO @ Sun, 21 Jun 2020 20:59:15: Done! pass1 - making usageList (138 chroms): 1 millis pass2 - checking and writing primary data (276 records, 4 fields): 6 millis CompletedMACS2peakCalling