Job ID = 6456957 SRX = SRX4158181 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T11:27:57 prefetch.2.10.7: 1) Downloading 'SRR7253461'... 2020-06-21T11:27:57 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T11:32:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T11:32:07 prefetch.2.10.7: 1) 'SRR7253461' was downloaded successfully Read 16031498 spots for SRR7253461/SRR7253461.sra Written 16031498 spots for SRR7253461/SRR7253461.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: 00:04:51 16031498 reads; of these: 16031498 (100.00%) were unpaired; of these: 723608 (4.51%) aligned 0 times 8454866 (52.74%) aligned exactly 1 time 6853024 (42.75%) aligned >1 times 95.49% overall alignment rate Time searching: 00:04:51 Overall time: 00:04:51 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] 2659106 / 15307890 = 0.1737 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 20:41:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.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 20:41:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:41:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:41:46: 1000000 INFO @ Sun, 21 Jun 2020 20:41:51: 2000000 INFO @ Sun, 21 Jun 2020 20:41:57: 3000000 INFO @ Sun, 21 Jun 2020 20:42:03: 4000000 INFO @ Sun, 21 Jun 2020 20:42:08: 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 20:42:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.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 20:42:10: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:42:10: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:42:14: 6000000 INFO @ Sun, 21 Jun 2020 20:42:16: 1000000 INFO @ Sun, 21 Jun 2020 20:42:20: 7000000 INFO @ Sun, 21 Jun 2020 20:42:22: 2000000 INFO @ Sun, 21 Jun 2020 20:42:27: 8000000 INFO @ Sun, 21 Jun 2020 20:42:28: 3000000 INFO @ Sun, 21 Jun 2020 20:42:33: 9000000 INFO @ Sun, 21 Jun 2020 20:42:34: 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 20:42:39: 5000000 INFO @ Sun, 21 Jun 2020 20:42:40: 10000000 INFO @ Sun, 21 Jun 2020 20:42:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.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 20:42:40: #1 read tag files... INFO @ Sun, 21 Jun 2020 20:42:40: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 20:42:45: 6000000 INFO @ Sun, 21 Jun 2020 20:42:46: 1000000 INFO @ Sun, 21 Jun 2020 20:42:46: 11000000 INFO @ Sun, 21 Jun 2020 20:42:51: 7000000 INFO @ Sun, 21 Jun 2020 20:42:52: 2000000 INFO @ Sun, 21 Jun 2020 20:42:52: 12000000 INFO @ Sun, 21 Jun 2020 20:42:57: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:42:57: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:42:57: #1 total tags in treatment: 12648784 INFO @ Sun, 21 Jun 2020 20:42:57: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:42:57: #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 20:42:57: #1 tags after filtering in treatment: 12648741 INFO @ Sun, 21 Jun 2020 20:42:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:42:57: #1 finished! INFO @ Sun, 21 Jun 2020 20:42:57: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:42:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:42:57: 8000000 INFO @ Sun, 21 Jun 2020 20:42:58: 3000000 INFO @ Sun, 21 Jun 2020 20:42:58: #2 number of paired peaks: 1657 INFO @ Sun, 21 Jun 2020 20:42:58: start model_add_line... INFO @ Sun, 21 Jun 2020 20:42:58: start X-correlation... INFO @ Sun, 21 Jun 2020 20:42:58: end of X-cor INFO @ Sun, 21 Jun 2020 20:42:58: #2 finished! INFO @ Sun, 21 Jun 2020 20:42:58: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 20:42:58: #2 alternative fragment length(s) may be 3,60 bps INFO @ Sun, 21 Jun 2020 20:42:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.05_model.r WARNING @ Sun, 21 Jun 2020 20:42:58: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:42:58: #2 You may need to consider one of the other alternative d(s): 3,60 WARNING @ Sun, 21 Jun 2020 20:42:58: #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 20:42:58: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:42:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:43:03: 4000000 INFO @ Sun, 21 Jun 2020 20:43:04: 9000000 INFO @ Sun, 21 Jun 2020 20:43:09: 5000000 INFO @ Sun, 21 Jun 2020 20:43:10: 10000000 INFO @ Sun, 21 Jun 2020 20:43:15: 6000000 INFO @ Sun, 21 Jun 2020 20:43:17: 11000000 INFO @ Sun, 21 Jun 2020 20:43:21: 7000000 INFO @ Sun, 21 Jun 2020 20:43:23: 12000000 INFO @ Sun, 21 Jun 2020 20:43:24: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:43:27: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:43:27: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:43:27: #1 total tags in treatment: 12648784 INFO @ Sun, 21 Jun 2020 20:43:27: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:43:27: #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 20:43:27: 8000000 INFO @ Sun, 21 Jun 2020 20:43:27: #1 tags after filtering in treatment: 12648741 INFO @ Sun, 21 Jun 2020 20:43:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:43:27: #1 finished! INFO @ Sun, 21 Jun 2020 20:43:27: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:43:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:43:28: #2 number of paired peaks: 1657 INFO @ Sun, 21 Jun 2020 20:43:28: start model_add_line... INFO @ Sun, 21 Jun 2020 20:43:29: start X-correlation... INFO @ Sun, 21 Jun 2020 20:43:29: end of X-cor INFO @ Sun, 21 Jun 2020 20:43:29: #2 finished! INFO @ Sun, 21 Jun 2020 20:43:29: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 20:43:29: #2 alternative fragment length(s) may be 3,60 bps INFO @ Sun, 21 Jun 2020 20:43:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.10_model.r WARNING @ Sun, 21 Jun 2020 20:43:29: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:43:29: #2 You may need to consider one of the other alternative d(s): 3,60 WARNING @ Sun, 21 Jun 2020 20:43:29: #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 20:43:29: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:43:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 20:43:33: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 20:43:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.05_peaks.xls INFO @ Sun, 21 Jun 2020 20:43:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:43:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.05_summits.bed INFO @ Sun, 21 Jun 2020 20:43:36: Done! pass1 - making usageList (782 chroms): 2 millis pass2 - checking and writing primary data (3772 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:43:39: 10000000 INFO @ Sun, 21 Jun 2020 20:43:45: 11000000 INFO @ Sun, 21 Jun 2020 20:43:51: 12000000 INFO @ Sun, 21 Jun 2020 20:43:53: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:43:55: #1 tag size is determined as 49 bps INFO @ Sun, 21 Jun 2020 20:43:55: #1 tag size = 49 INFO @ Sun, 21 Jun 2020 20:43:55: #1 total tags in treatment: 12648784 INFO @ Sun, 21 Jun 2020 20:43:55: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 20:43:55: #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 20:43:56: #1 tags after filtering in treatment: 12648741 INFO @ Sun, 21 Jun 2020 20:43:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 20:43:56: #1 finished! INFO @ Sun, 21 Jun 2020 20:43:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 20:43:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 20:43:57: #2 number of paired peaks: 1657 INFO @ Sun, 21 Jun 2020 20:43:57: start model_add_line... INFO @ Sun, 21 Jun 2020 20:43:57: start X-correlation... INFO @ Sun, 21 Jun 2020 20:43:57: end of X-cor INFO @ Sun, 21 Jun 2020 20:43:57: #2 finished! INFO @ Sun, 21 Jun 2020 20:43:57: #2 predicted fragment length is 60 bps INFO @ Sun, 21 Jun 2020 20:43:57: #2 alternative fragment length(s) may be 3,60 bps INFO @ Sun, 21 Jun 2020 20:43:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.20_model.r WARNING @ Sun, 21 Jun 2020 20:43:57: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 20:43:57: #2 You may need to consider one of the other alternative d(s): 3,60 WARNING @ Sun, 21 Jun 2020 20:43:57: #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 20:43:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 20:43:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 20:44:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.10_peaks.xls INFO @ Sun, 21 Jun 2020 20:44:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:44:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.10_summits.bed INFO @ Sun, 21 Jun 2020 20:44:04: Done! pass1 - making usageList (599 chroms): 1 millis pass2 - checking and writing primary data (2175 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 20:44:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 20:44:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.20_peaks.xls INFO @ Sun, 21 Jun 2020 20:44:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 20:44:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX4158181/SRX4158181.20_summits.bed INFO @ Sun, 21 Jun 2020 20:44:33: Done! pass1 - making usageList (319 chroms): 1 millis pass2 - checking and writing primary data (804 records, 4 fields): 9 millis CompletedMACS2peakCalling