Job ID = 6455102 SRX = SRX2692977 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T09:49:25 prefetch.2.10.7: 1) Downloading 'SRR5398176'... 2020-06-21T09:49:25 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T09:59:22 prefetch.2.10.7: HTTPS download succeed 2020-06-21T09:59:22 prefetch.2.10.7: 1) 'SRR5398176' was downloaded successfully 2020-06-21T09:59:22 prefetch.2.10.7: 'SRR5398176' has 0 unresolved dependencies Read 72549462 spots for SRR5398176/SRR5398176.sra Written 72549462 spots for SRR5398176/SRR5398176.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: 00:41:10 72549462 reads; of these: 72549462 (100.00%) were unpaired; of these: 14179931 (19.55%) aligned 0 times 15700500 (21.64%) aligned exactly 1 time 42669031 (58.81%) aligned >1 times 80.45% overall alignment rate Time searching: 00:41:10 Overall time: 00:41:10 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 24 files... [bam_rmdupse_core] 37972868 / 58369531 = 0.6506 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 19:55:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.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 19:55:34: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:55:34: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:55:39: 1000000 INFO @ Sun, 21 Jun 2020 19:55:45: 2000000 INFO @ Sun, 21 Jun 2020 19:55:51: 3000000 INFO @ Sun, 21 Jun 2020 19:55:57: 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 19:56:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.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 19:56:02: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:56:02: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:56:03: 5000000 INFO @ Sun, 21 Jun 2020 19:56:08: 1000000 INFO @ Sun, 21 Jun 2020 19:56:09: 6000000 INFO @ Sun, 21 Jun 2020 19:56:13: 2000000 INFO @ Sun, 21 Jun 2020 19:56:15: 7000000 INFO @ Sun, 21 Jun 2020 19:56:18: 3000000 INFO @ Sun, 21 Jun 2020 19:56:21: 8000000 INFO @ Sun, 21 Jun 2020 19:56:24: 4000000 INFO @ Sun, 21 Jun 2020 19:56:26: 9000000 INFO @ Sun, 21 Jun 2020 19:56:29: 5000000 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 19:56:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.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 19:56:32: #1 read tag files... INFO @ Sun, 21 Jun 2020 19:56:32: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 19:56:32: 10000000 INFO @ Sun, 21 Jun 2020 19:56:34: 6000000 INFO @ Sun, 21 Jun 2020 19:56:38: 11000000 INFO @ Sun, 21 Jun 2020 19:56:38: 1000000 INFO @ Sun, 21 Jun 2020 19:56:39: 7000000 INFO @ Sun, 21 Jun 2020 19:56:44: 12000000 INFO @ Sun, 21 Jun 2020 19:56:45: 2000000 INFO @ Sun, 21 Jun 2020 19:56:45: 8000000 INFO @ Sun, 21 Jun 2020 19:56:50: 13000000 INFO @ Sun, 21 Jun 2020 19:56:50: 9000000 INFO @ Sun, 21 Jun 2020 19:56:51: 3000000 INFO @ Sun, 21 Jun 2020 19:56:55: 10000000 INFO @ Sun, 21 Jun 2020 19:56:56: 14000000 INFO @ Sun, 21 Jun 2020 19:56:57: 4000000 INFO @ Sun, 21 Jun 2020 19:57:00: 11000000 INFO @ Sun, 21 Jun 2020 19:57:02: 15000000 INFO @ Sun, 21 Jun 2020 19:57:03: 5000000 INFO @ Sun, 21 Jun 2020 19:57:06: 12000000 INFO @ Sun, 21 Jun 2020 19:57:08: 16000000 INFO @ Sun, 21 Jun 2020 19:57:09: 6000000 INFO @ Sun, 21 Jun 2020 19:57:11: 13000000 INFO @ Sun, 21 Jun 2020 19:57:14: 17000000 INFO @ Sun, 21 Jun 2020 19:57:15: 7000000 INFO @ Sun, 21 Jun 2020 19:57:16: 14000000 INFO @ Sun, 21 Jun 2020 19:57:20: 18000000 INFO @ Sun, 21 Jun 2020 19:57:21: 8000000 INFO @ Sun, 21 Jun 2020 19:57:22: 15000000 INFO @ Sun, 21 Jun 2020 19:57:26: 19000000 INFO @ Sun, 21 Jun 2020 19:57:27: 16000000 INFO @ Sun, 21 Jun 2020 19:57:27: 9000000 INFO @ Sun, 21 Jun 2020 19:57:32: 20000000 INFO @ Sun, 21 Jun 2020 19:57:32: 17000000 INFO @ Sun, 21 Jun 2020 19:57:33: 10000000 INFO @ Sun, 21 Jun 2020 19:57:35: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 19:57:35: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 19:57:35: #1 total tags in treatment: 20396663 INFO @ Sun, 21 Jun 2020 19:57:35: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:57:35: #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 19:57:35: #1 tags after filtering in treatment: 20396658 INFO @ Sun, 21 Jun 2020 19:57:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:57:35: #1 finished! INFO @ Sun, 21 Jun 2020 19:57:35: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:57:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:57:37: #2 number of paired peaks: 3129 INFO @ Sun, 21 Jun 2020 19:57:37: start model_add_line... INFO @ Sun, 21 Jun 2020 19:57:37: start X-correlation... INFO @ Sun, 21 Jun 2020 19:57:37: end of X-cor INFO @ Sun, 21 Jun 2020 19:57:37: #2 finished! INFO @ Sun, 21 Jun 2020 19:57:37: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 19:57:37: #2 alternative fragment length(s) may be 3,79 bps INFO @ Sun, 21 Jun 2020 19:57:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.05_model.r WARNING @ Sun, 21 Jun 2020 19:57:37: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:57:37: #2 You may need to consider one of the other alternative d(s): 3,79 WARNING @ Sun, 21 Jun 2020 19:57:37: #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 19:57:37: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:57:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:57:38: 18000000 INFO @ Sun, 21 Jun 2020 19:57:39: 11000000 INFO @ Sun, 21 Jun 2020 19:57:43: 19000000 INFO @ Sun, 21 Jun 2020 19:57:45: 12000000 INFO @ Sun, 21 Jun 2020 19:57:48: 20000000 INFO @ Sun, 21 Jun 2020 19:57:51: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 19:57:51: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 19:57:51: #1 total tags in treatment: 20396663 INFO @ Sun, 21 Jun 2020 19:57:51: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:57:51: #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 19:57:51: #1 tags after filtering in treatment: 20396658 INFO @ Sun, 21 Jun 2020 19:57:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:57:51: #1 finished! INFO @ Sun, 21 Jun 2020 19:57:51: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:57:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:57:51: 13000000 INFO @ Sun, 21 Jun 2020 19:57:53: #2 number of paired peaks: 3129 INFO @ Sun, 21 Jun 2020 19:57:53: start model_add_line... INFO @ Sun, 21 Jun 2020 19:57:53: start X-correlation... INFO @ Sun, 21 Jun 2020 19:57:53: end of X-cor INFO @ Sun, 21 Jun 2020 19:57:53: #2 finished! INFO @ Sun, 21 Jun 2020 19:57:53: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 19:57:53: #2 alternative fragment length(s) may be 3,79 bps INFO @ Sun, 21 Jun 2020 19:57:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.10_model.r WARNING @ Sun, 21 Jun 2020 19:57:53: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:57:53: #2 You may need to consider one of the other alternative d(s): 3,79 WARNING @ Sun, 21 Jun 2020 19:57:53: #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 19:57:53: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:57:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:57:57: 14000000 INFO @ Sun, 21 Jun 2020 19:58:03: 15000000 INFO @ Sun, 21 Jun 2020 19:58:10: 16000000 INFO @ Sun, 21 Jun 2020 19:58:16: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 19:58:16: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:58:22: 18000000 INFO @ Sun, 21 Jun 2020 19:58:28: 19000000 INFO @ Sun, 21 Jun 2020 19:58:31: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:58:34: 20000000 INFO @ Sun, 21 Jun 2020 19:58:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.05_peaks.xls INFO @ Sun, 21 Jun 2020 19:58:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:58:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.05_summits.bed INFO @ Sun, 21 Jun 2020 19:58:36: Done! pass1 - making usageList (1046 chroms): 3 millis pass2 - checking and writing primary data (13352 records, 4 fields): 37 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 19:58:37: #1 tag size is determined as 75 bps INFO @ Sun, 21 Jun 2020 19:58:37: #1 tag size = 75 INFO @ Sun, 21 Jun 2020 19:58:37: #1 total tags in treatment: 20396663 INFO @ Sun, 21 Jun 2020 19:58:37: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 19:58:37: #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 19:58:37: #1 tags after filtering in treatment: 20396658 INFO @ Sun, 21 Jun 2020 19:58:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 19:58:37: #1 finished! INFO @ Sun, 21 Jun 2020 19:58:37: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 19:58:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 19:58:39: #2 number of paired peaks: 3129 INFO @ Sun, 21 Jun 2020 19:58:39: start model_add_line... INFO @ Sun, 21 Jun 2020 19:58:39: start X-correlation... INFO @ Sun, 21 Jun 2020 19:58:39: end of X-cor INFO @ Sun, 21 Jun 2020 19:58:39: #2 finished! INFO @ Sun, 21 Jun 2020 19:58:39: #2 predicted fragment length is 79 bps INFO @ Sun, 21 Jun 2020 19:58:39: #2 alternative fragment length(s) may be 3,79 bps INFO @ Sun, 21 Jun 2020 19:58:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.20_model.r WARNING @ Sun, 21 Jun 2020 19:58:39: #2 Since the d (79) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 19:58:39: #2 You may need to consider one of the other alternative d(s): 3,79 WARNING @ Sun, 21 Jun 2020 19:58:39: #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 19:58:39: #3 Call peaks... INFO @ Sun, 21 Jun 2020 19:58:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 19:58:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.10_peaks.xls INFO @ Sun, 21 Jun 2020 19:58:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:58:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.10_summits.bed INFO @ Sun, 21 Jun 2020 19:58:50: Done! pass1 - making usageList (888 chroms): 2 millis pass2 - checking and writing primary data (6947 records, 4 fields): 28 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 19:59:18: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 19:59:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.20_peaks.xls INFO @ Sun, 21 Jun 2020 19:59:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 19:59:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX2692977/SRX2692977.20_summits.bed INFO @ Sun, 21 Jun 2020 19:59:36: Done! pass1 - making usageList (772 chroms): 1 millis pass2 - checking and writing primary data (3313 records, 4 fields): 22 millis CompletedMACS2peakCalling