Job ID = 6457036 SRX = SRX4370066 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:32:55 prefetch.2.10.7: 1) Downloading 'SRR7500643'... 2020-06-21T11:32:55 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:34:11 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:34:11 prefetch.2.10.7: 'SRR7500643' is valid 2020-06-21T11:34:11 prefetch.2.10.7: 1) 'SRR7500643' was downloaded successfully 2020-06-21T11:34:11 prefetch.2.10.7: 'SRR7500643' has 0 unresolved dependencies Read 10690945 spots for SRR7500643/SRR7500643.sra Written 10690945 spots for SRR7500643/SRR7500643.sra fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:54 10690945 reads; of these: 10690945 (100.00%) were unpaired; of these: 350596 (3.28%) aligned 0 times 7248070 (67.80%) aligned exactly 1 time 3092279 (28.92%) aligned >1 times 96.72% overall alignment rate Time searching: 00:02:55 Overall time: 00:02:55 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] 2816534 / 10340349 = 0.2724 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 20:40:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.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 20:40:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:40:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:40:21: 1000000 INFO @ Sun, 21 Jun 2020 20:40:27: 2000000 INFO @ Sun, 21 Jun 2020 20:40:34: 3000000 INFO @ Sun, 21 Jun 2020 20:40:40: 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 20:40:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.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 20:40:44: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:40:44: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:40:47: 5000000 INFO @ Sun, 21 Jun 2020 20:40:50: 1000000 INFO @ Sun, 21 Jun 2020 20:40:53: 6000000 INFO @ Sun, 21 Jun 2020 20:40:57: 2000000 INFO @ Sun, 21 Jun 2020 20:41:01: 7000000 INFO @ Sun, 21 Jun 2020 20:41:03: 3000000 INFO @ Sun, 21 Jun 2020 20:41:04: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:41:04: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:41:04: #1 total tags in treatment: 7523815 INFO @ Sun, 21 Jun 2020 20:41:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:41:04: #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 20:41:05: #1 tags after filtering in treatment: 7523714 INFO @ Sun, 21 Jun 2020 20:41:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:41:05: #1 finished! INFO @ Sun, 21 Jun 2020 20:41:05: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:41:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:41:05: #2 number of paired peaks: 1099 INFO @ Sun, 21 Jun 2020 20:41:05: start model_add_line... INFO @ Sun, 21 Jun 2020 20:41:05: start X-correlation... INFO @ Sun, 21 Jun 2020 20:41:06: end of X-cor INFO @ Sun, 21 Jun 2020 20:41:06: #2 finished! INFO @ Sun, 21 Jun 2020 20:41:06: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 20:41:06: #2 alternative fragment length(s) may be 3,47,556 bps INFO @ Sun, 21 Jun 2020 20:41:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.05_model.r WARNING @ Sun, 21 Jun 2020 20:41:06: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:41:06: #2 You may need to consider one of the other alternative d(s): 3,47,556 WARNING @ Sun, 21 Jun 2020 20:41:06: #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 20:41:06: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:41:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:41:09: 4000000 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 20:41:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.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 20:41:14: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:41:14: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:41:15: 5000000 INFO @ Sun, 21 Jun 2020 20:41:21: 1000000 INFO @ Sun, 21 Jun 2020 20:41:21: 6000000 INFO @ Sun, 21 Jun 2020 20:41:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:41:28: 2000000 INFO @ Sun, 21 Jun 2020 20:41:28: 7000000 INFO @ Sun, 21 Jun 2020 20:41:32: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:41:32: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:41:32: #1 total tags in treatment: 7523815 INFO @ Sun, 21 Jun 2020 20:41:32: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:41:32: #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 20:41:32: #1 tags after filtering in treatment: 7523714 INFO @ Sun, 21 Jun 2020 20:41:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:41:32: #1 finished! INFO @ Sun, 21 Jun 2020 20:41:32: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:41:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:41:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:41:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:41:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.05_summits.bed INFO @ Sun, 21 Jun 2020 20:41:32: Done! pass1 - making usageList (474 chroms): 1 millis pass2 - checking and writing primary data (1640 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:41:33: #2 number of paired peaks: 1099 INFO @ Sun, 21 Jun 2020 20:41:33: start model_add_line... INFO @ Sun, 21 Jun 2020 20:41:33: start X-correlation... INFO @ Sun, 21 Jun 2020 20:41:33: end of X-cor INFO @ Sun, 21 Jun 2020 20:41:33: #2 finished! INFO @ Sun, 21 Jun 2020 20:41:33: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 20:41:33: #2 alternative fragment length(s) may be 3,47,556 bps INFO @ Sun, 21 Jun 2020 20:41:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.10_model.r WARNING @ Sun, 21 Jun 2020 20:41:33: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:41:33: #2 You may need to consider one of the other alternative d(s): 3,47,556 WARNING @ Sun, 21 Jun 2020 20:41:33: #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 20:41:33: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:41:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:41:34: 3000000 INFO @ Sun, 21 Jun 2020 20:41:41: 4000000 INFO @ Sun, 21 Jun 2020 20:41:47: 5000000 INFO @ Sun, 21 Jun 2020 20:41:50: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:41:54: 6000000 INFO @ Sun, 21 Jun 2020 20:41:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:41:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:41:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.10_summits.bed INFO @ Sun, 21 Jun 2020 20:41:58: Done! pass1 - making usageList (280 chroms): 1 millis pass2 - checking and writing primary data (669 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:42:01: 7000000 INFO @ Sun, 21 Jun 2020 20:42:04: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:42:04: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:42:04: #1 total tags in treatment: 7523815 INFO @ Sun, 21 Jun 2020 20:42:04: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:42:04: #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 20:42:04: #1 tags after filtering in treatment: 7523714 INFO @ Sun, 21 Jun 2020 20:42:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:42:04: #1 finished! INFO @ Sun, 21 Jun 2020 20:42:04: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:42:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:42:05: #2 number of paired peaks: 1099 INFO @ Sun, 21 Jun 2020 20:42:05: start model_add_line... INFO @ Sun, 21 Jun 2020 20:42:05: start X-correlation... INFO @ Sun, 21 Jun 2020 20:42:05: end of X-cor INFO @ Sun, 21 Jun 2020 20:42:05: #2 finished! INFO @ Sun, 21 Jun 2020 20:42:05: #2 predicted fragment length is 47 bps INFO @ Sun, 21 Jun 2020 20:42:05: #2 alternative fragment length(s) may be 3,47,556 bps INFO @ Sun, 21 Jun 2020 20:42:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.20_model.r WARNING @ Sun, 21 Jun 2020 20:42:05: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:42:05: #2 You may need to consider one of the other alternative d(s): 3,47,556 WARNING @ Sun, 21 Jun 2020 20:42:05: #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 20:42:05: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:42:05: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:42:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:42:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:42:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:42:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4370066/SRX4370066.20_summits.bed INFO @ Sun, 21 Jun 2020 20:42:31: Done! pass1 - making usageList (107 chroms): 0 millis pass2 - checking and writing primary data (192 records, 4 fields): 4 millis CompletedMACS2peakCalling