Job ID = 6498642 SRX = SRX647441 Genome = dm3 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-25T23:31:46 prefetch.2.10.7: 1) Downloading 'SRR1508424'... 2020-06-25T23:31:46 prefetch.2.10.7: Downloading via HTTPS... 2020-06-25T23:36:05 prefetch.2.10.7: HTTPS download succeed 2020-06-25T23:36:05 prefetch.2.10.7: 1) 'SRR1508424' was downloaded successfully Read 17443450 spots for SRR1508424/SRR1508424.sra Written 17443450 spots for SRR1508424/SRR1508424.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: 00:11:23 17443450 reads; of these: 17443450 (100.00%) were unpaired; of these: 3865979 (22.16%) aligned 0 times 10299327 (59.04%) aligned exactly 1 time 3278144 (18.79%) aligned >1 times 77.84% overall alignment rate Time searching: 00:11:23 Overall time: 00:11:23 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 8 files... [bam_rmdupse_core] 9506311 / 13577471 = 0.7002 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 08:53:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.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 08:53:32: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:53:32: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:53:40: 1000000 INFO @ Fri, 26 Jun 2020 08:53:47: 2000000 INFO @ Fri, 26 Jun 2020 08:53:55: 3000000 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 08:54:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.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 08:54:02: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:54:02: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:54:03: 4000000 INFO @ Fri, 26 Jun 2020 08:54:03: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 08:54:03: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 08:54:03: #1 total tags in treatment: 4071160 INFO @ Fri, 26 Jun 2020 08:54:03: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:54:03: #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 08:54:03: #1 tags after filtering in treatment: 4071160 INFO @ Fri, 26 Jun 2020 08:54:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:54:03: #1 finished! INFO @ Fri, 26 Jun 2020 08:54:03: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:54:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:54:04: #2 number of paired peaks: 1116 INFO @ Fri, 26 Jun 2020 08:54:04: start model_add_line... INFO @ Fri, 26 Jun 2020 08:54:04: start X-correlation... INFO @ Fri, 26 Jun 2020 08:54:04: end of X-cor INFO @ Fri, 26 Jun 2020 08:54:04: #2 finished! INFO @ Fri, 26 Jun 2020 08:54:04: #2 predicted fragment length is 93 bps INFO @ Fri, 26 Jun 2020 08:54:04: #2 alternative fragment length(s) may be 93 bps INFO @ Fri, 26 Jun 2020 08:54:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.05_model.r WARNING @ Fri, 26 Jun 2020 08:54:04: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:54:04: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Fri, 26 Jun 2020 08:54:04: #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 08:54:04: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:54:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:54:10: 1000000 INFO @ Fri, 26 Jun 2020 08:54:12: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:54:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.05_peaks.xls INFO @ Fri, 26 Jun 2020 08:54:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.05_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:54:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.05_summits.bed INFO @ Fri, 26 Jun 2020 08:54:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2770 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:54:17: 2000000 INFO @ Fri, 26 Jun 2020 08:54:25: 3000000 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 08:54:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.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 08:54:32: #1 read tag files... INFO @ Fri, 26 Jun 2020 08:54:32: #1 read treatment tags... INFO @ Fri, 26 Jun 2020 08:54:33: 4000000 INFO @ Fri, 26 Jun 2020 08:54:33: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 08:54:33: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 08:54:33: #1 total tags in treatment: 4071160 INFO @ Fri, 26 Jun 2020 08:54:33: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:54:33: #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 08:54:33: #1 tags after filtering in treatment: 4071160 INFO @ Fri, 26 Jun 2020 08:54:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:54:33: #1 finished! INFO @ Fri, 26 Jun 2020 08:54:33: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:54:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:54:34: #2 number of paired peaks: 1116 INFO @ Fri, 26 Jun 2020 08:54:34: start model_add_line... INFO @ Fri, 26 Jun 2020 08:54:34: start X-correlation... INFO @ Fri, 26 Jun 2020 08:54:34: end of X-cor INFO @ Fri, 26 Jun 2020 08:54:34: #2 finished! INFO @ Fri, 26 Jun 2020 08:54:34: #2 predicted fragment length is 93 bps INFO @ Fri, 26 Jun 2020 08:54:34: #2 alternative fragment length(s) may be 93 bps INFO @ Fri, 26 Jun 2020 08:54:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.10_model.r WARNING @ Fri, 26 Jun 2020 08:54:34: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:54:34: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Fri, 26 Jun 2020 08:54:34: #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 08:54:34: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:54:34: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:54:40: 1000000 INFO @ Fri, 26 Jun 2020 08:54:42: #3 Call peaks for each chromosome... INFO @ Fri, 26 Jun 2020 08:54:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.10_peaks.xls INFO @ Fri, 26 Jun 2020 08:54:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.10_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:54:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.10_summits.bed INFO @ Fri, 26 Jun 2020 08:54:47: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1362 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 26 Jun 2020 08:54:48: 2000000 INFO @ Fri, 26 Jun 2020 08:54:55: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 26 Jun 2020 08:55:03: 4000000 INFO @ Fri, 26 Jun 2020 08:55:03: #1 tag size is determined as 100 bps INFO @ Fri, 26 Jun 2020 08:55:03: #1 tag size = 100 INFO @ Fri, 26 Jun 2020 08:55:03: #1 total tags in treatment: 4071160 INFO @ Fri, 26 Jun 2020 08:55:03: #1 user defined the maximum tags... INFO @ Fri, 26 Jun 2020 08:55:03: #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 08:55:03: #1 tags after filtering in treatment: 4071160 INFO @ Fri, 26 Jun 2020 08:55:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 26 Jun 2020 08:55:03: #1 finished! INFO @ Fri, 26 Jun 2020 08:55:03: #2 Build Peak Model... INFO @ Fri, 26 Jun 2020 08:55:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 26 Jun 2020 08:55:04: #2 number of paired peaks: 1116 INFO @ Fri, 26 Jun 2020 08:55:04: start model_add_line... INFO @ Fri, 26 Jun 2020 08:55:04: start X-correlation... INFO @ Fri, 26 Jun 2020 08:55:04: end of X-cor INFO @ Fri, 26 Jun 2020 08:55:04: #2 finished! INFO @ Fri, 26 Jun 2020 08:55:04: #2 predicted fragment length is 93 bps INFO @ Fri, 26 Jun 2020 08:55:04: #2 alternative fragment length(s) may be 93 bps INFO @ Fri, 26 Jun 2020 08:55:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.20_model.r WARNING @ Fri, 26 Jun 2020 08:55:04: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 26 Jun 2020 08:55:04: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Fri, 26 Jun 2020 08:55:04: #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 08:55:04: #3 Call peaks... INFO @ Fri, 26 Jun 2020 08:55:04: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 26 Jun 2020 08:55:12: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Fri, 26 Jun 2020 08:55:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.20_peaks.xls INFO @ Fri, 26 Jun 2020 08:55:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.20_peaks.narrowPeak INFO @ Fri, 26 Jun 2020 08:55:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX647441/SRX647441.20_summits.bed INFO @ Fri, 26 Jun 2020 08:55:17: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (817 records, 4 fields): 2 millis CompletedMACS2peakCalling