Job ID = 6458287 SRX = SRX5011044 Genome = dm6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-21T12:18:22 prefetch.2.10.7: 1) Downloading 'SRR8191493'... 2020-06-21T12:18:22 prefetch.2.10.7: Downloading via HTTPS... 2020-06-21T12:20:07 prefetch.2.10.7: HTTPS download succeed 2020-06-21T12:20:08 prefetch.2.10.7: 'SRR8191493' is valid 2020-06-21T12:20:08 prefetch.2.10.7: 1) 'SRR8191493' was downloaded successfully 2020-06-21T12:20:08 prefetch.2.10.7: 'SRR8191493' has 0 unresolved dependencies Read 24560848 spots for SRR8191493/SRR8191493.sra Written 24560848 spots for SRR8191493/SRR8191493.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: 00:06:57 24560848 reads; of these: 24560848 (100.00%) were unpaired; of these: 586749 (2.39%) aligned 0 times 16870602 (68.69%) aligned exactly 1 time 7103497 (28.92%) aligned >1 times 97.61% overall alignment rate Time searching: 00:06:57 Overall time: 00:06:57 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 12 files... [bam_rmdupse_core] 12411037 / 23974099 = 0.5177 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 21:31:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.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 21:31:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:31:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:32:03: 1000000 INFO @ Sun, 21 Jun 2020 21:32:08: 2000000 INFO @ Sun, 21 Jun 2020 21:32:13: 3000000 INFO @ Sun, 21 Jun 2020 21:32:18: 4000000 INFO @ Sun, 21 Jun 2020 21:32:23: 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 21:32:27: 6000000 INFO @ Sun, 21 Jun 2020 21:32:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.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 21:32:28: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:32:28: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:32:32: 7000000 INFO @ Sun, 21 Jun 2020 21:32:33: 1000000 INFO @ Sun, 21 Jun 2020 21:32:37: 8000000 INFO @ Sun, 21 Jun 2020 21:32:39: 2000000 INFO @ Sun, 21 Jun 2020 21:32:43: 9000000 INFO @ Sun, 21 Jun 2020 21:32:44: 3000000 INFO @ Sun, 21 Jun 2020 21:32:48: 10000000 INFO @ Sun, 21 Jun 2020 21:32:49: 4000000 INFO @ Sun, 21 Jun 2020 21:32:53: 11000000 INFO @ Sun, 21 Jun 2020 21:32:54: 5000000 INFO @ Sun, 21 Jun 2020 21:32:56: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:32:56: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:32:56: #1 total tags in treatment: 11563062 INFO @ Sun, 21 Jun 2020 21:32:56: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:32:56: #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 21:32:56: #1 tags after filtering in treatment: 11562997 INFO @ Sun, 21 Jun 2020 21:32:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:32:56: #1 finished! INFO @ Sun, 21 Jun 2020 21:32:56: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:32:56: #2 looking for paired plus/minus strand peaks... 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 21:32:57: #2 number of paired peaks: 2105 INFO @ Sun, 21 Jun 2020 21:32:57: start model_add_line... INFO @ Sun, 21 Jun 2020 21:32:57: start X-correlation... INFO @ Sun, 21 Jun 2020 21:32:57: end of X-cor INFO @ Sun, 21 Jun 2020 21:32:57: #2 finished! INFO @ Sun, 21 Jun 2020 21:32:57: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 21:32:57: #2 alternative fragment length(s) may be 3,65 bps INFO @ Sun, 21 Jun 2020 21:32:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.05_model.r WARNING @ Sun, 21 Jun 2020 21:32:57: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:32:57: #2 You may need to consider one of the other alternative d(s): 3,65 WARNING @ Sun, 21 Jun 2020 21:32:57: #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 21:32:57: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:32:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:32:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.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 21:32:58: #1 read tag files... INFO @ Sun, 21 Jun 2020 21:32:58: #1 read treatment tags... INFO @ Sun, 21 Jun 2020 21:32:59: 6000000 INFO @ Sun, 21 Jun 2020 21:33:04: 1000000 INFO @ Sun, 21 Jun 2020 21:33:04: 7000000 INFO @ Sun, 21 Jun 2020 21:33:09: 2000000 INFO @ Sun, 21 Jun 2020 21:33:09: 8000000 INFO @ Sun, 21 Jun 2020 21:33:14: 3000000 INFO @ Sun, 21 Jun 2020 21:33:15: 9000000 INFO @ Sun, 21 Jun 2020 21:33:19: 4000000 INFO @ Sun, 21 Jun 2020 21:33:20: 10000000 INFO @ Sun, 21 Jun 2020 21:33:21: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:33:25: 5000000 INFO @ Sun, 21 Jun 2020 21:33:25: 11000000 INFO @ Sun, 21 Jun 2020 21:33:28: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:33:28: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:33:28: #1 total tags in treatment: 11563062 INFO @ Sun, 21 Jun 2020 21:33:28: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:33:28: #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 21:33:29: #1 tags after filtering in treatment: 11562997 INFO @ Sun, 21 Jun 2020 21:33:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:33:29: #1 finished! INFO @ Sun, 21 Jun 2020 21:33:29: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:33:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:33:30: #2 number of paired peaks: 2105 INFO @ Sun, 21 Jun 2020 21:33:30: start model_add_line... INFO @ Sun, 21 Jun 2020 21:33:30: start X-correlation... INFO @ Sun, 21 Jun 2020 21:33:30: end of X-cor INFO @ Sun, 21 Jun 2020 21:33:30: #2 finished! INFO @ Sun, 21 Jun 2020 21:33:30: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 21:33:30: #2 alternative fragment length(s) may be 3,65 bps INFO @ Sun, 21 Jun 2020 21:33:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.10_model.r WARNING @ Sun, 21 Jun 2020 21:33:30: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:33:30: #2 You may need to consider one of the other alternative d(s): 3,65 WARNING @ Sun, 21 Jun 2020 21:33:30: #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 21:33:30: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:33:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:33:30: 6000000 INFO @ Sun, 21 Jun 2020 21:33:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.05_peaks.xls INFO @ Sun, 21 Jun 2020 21:33:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.05_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:33:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.05_summits.bed INFO @ Sun, 21 Jun 2020 21:33:32: Done! pass1 - making usageList (784 chroms): 1 millis pass2 - checking and writing primary data (3941 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Sun, 21 Jun 2020 21:33:35: 7000000 INFO @ Sun, 21 Jun 2020 21:33:40: 8000000 INFO @ Sun, 21 Jun 2020 21:33:45: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 21 Jun 2020 21:33:50: 10000000 INFO @ Sun, 21 Jun 2020 21:33:54: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:33:55: 11000000 INFO @ Sun, 21 Jun 2020 21:33:58: #1 tag size is determined as 50 bps INFO @ Sun, 21 Jun 2020 21:33:58: #1 tag size = 50 INFO @ Sun, 21 Jun 2020 21:33:58: #1 total tags in treatment: 11563062 INFO @ Sun, 21 Jun 2020 21:33:58: #1 user defined the maximum tags... INFO @ Sun, 21 Jun 2020 21:33:58: #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 21:33:58: #1 tags after filtering in treatment: 11562997 INFO @ Sun, 21 Jun 2020 21:33:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 21 Jun 2020 21:33:58: #1 finished! INFO @ Sun, 21 Jun 2020 21:33:58: #2 Build Peak Model... INFO @ Sun, 21 Jun 2020 21:33:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 21 Jun 2020 21:33:59: #2 number of paired peaks: 2105 INFO @ Sun, 21 Jun 2020 21:33:59: start model_add_line... INFO @ Sun, 21 Jun 2020 21:33:59: start X-correlation... INFO @ Sun, 21 Jun 2020 21:33:59: end of X-cor INFO @ Sun, 21 Jun 2020 21:33:59: #2 finished! INFO @ Sun, 21 Jun 2020 21:33:59: #2 predicted fragment length is 65 bps INFO @ Sun, 21 Jun 2020 21:33:59: #2 alternative fragment length(s) may be 3,65 bps INFO @ Sun, 21 Jun 2020 21:33:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.20_model.r WARNING @ Sun, 21 Jun 2020 21:33:59: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 21 Jun 2020 21:33:59: #2 You may need to consider one of the other alternative d(s): 3,65 WARNING @ Sun, 21 Jun 2020 21:33:59: #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 21:33:59: #3 Call peaks... INFO @ Sun, 21 Jun 2020 21:33:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 21 Jun 2020 21:34:06: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.10_peaks.xls INFO @ Sun, 21 Jun 2020 21:34:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.10_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:34:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.10_summits.bed INFO @ Sun, 21 Jun 2020 21:34:06: Done! pass1 - making usageList (684 chroms): 2 millis pass2 - checking and writing primary data (2629 records, 4 fields): 30 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sun, 21 Jun 2020 21:34:23: #3 Call peaks for each chromosome... INFO @ Sun, 21 Jun 2020 21:34:34: #4 Write output xls file... /home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.20_peaks.xls INFO @ Sun, 21 Jun 2020 21:34:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.20_peaks.narrowPeak INFO @ Sun, 21 Jun 2020 21:34:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm6/SRX5011044/SRX5011044.20_summits.bed INFO @ Sun, 21 Jun 2020 21:34:34: Done! pass1 - making usageList (435 chroms): 1 millis pass2 - checking and writing primary data (1014 records, 4 fields): 13 millis CompletedMACS2peakCalling