Job ID = 6368728 SRX = SRX5402752 Genome = ce11 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-06-16T00:28:01 prefetch.2.10.7: 1) Downloading 'SRR8602986'... 2020-06-16T00:28:01 prefetch.2.10.7: Downloading via HTTPS... 2020-06-16T00:32:58 prefetch.2.10.7: HTTPS download succeed 2020-06-16T00:32:58 prefetch.2.10.7: 1) 'SRR8602986' was downloaded successfully Read 35077861 spots for SRR8602986/SRR8602986.sra Written 35077861 spots for SRR8602986/SRR8602986.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: 00:08:05 35077861 reads; of these: 35077861 (100.00%) were unpaired; of these: 6692895 (19.08%) aligned 0 times 17469302 (49.80%) aligned exactly 1 time 10915664 (31.12%) aligned >1 times 80.92% overall alignment rate Time searching: 00:08:05 Overall time: 00:08:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 9622229 / 28384966 = 0.3390 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 @ Tue, 16 Jun 2020 09:49:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:49:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:07: 1000000 INFO @ Tue, 16 Jun 2020 09:49:12: 2000000 INFO @ Tue, 16 Jun 2020 09:49:18: 3000000 INFO @ Tue, 16 Jun 2020 09:49:24: 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 @ Tue, 16 Jun 2020 09:49:30: 5000000 INFO @ Tue, 16 Jun 2020 09:49:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:49:32: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:49:32: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:49:37: 6000000 INFO @ Tue, 16 Jun 2020 09:49:38: 1000000 INFO @ Tue, 16 Jun 2020 09:49:43: 7000000 INFO @ Tue, 16 Jun 2020 09:49:44: 2000000 INFO @ Tue, 16 Jun 2020 09:49:49: 8000000 INFO @ Tue, 16 Jun 2020 09:49:50: 3000000 INFO @ Tue, 16 Jun 2020 09:49:56: 9000000 INFO @ Tue, 16 Jun 2020 09:49:56: 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 @ Tue, 16 Jun 2020 09:50:02: 5000000 INFO @ Tue, 16 Jun 2020 09:50:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Tue, 16 Jun 2020 09:50:02: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:50:02: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:50:02: 10000000 INFO @ Tue, 16 Jun 2020 09:50:07: 6000000 INFO @ Tue, 16 Jun 2020 09:50:08: 1000000 INFO @ Tue, 16 Jun 2020 09:50:09: 11000000 INFO @ Tue, 16 Jun 2020 09:50:13: 7000000 INFO @ Tue, 16 Jun 2020 09:50:13: 2000000 INFO @ Tue, 16 Jun 2020 09:50:15: 12000000 INFO @ Tue, 16 Jun 2020 09:50:18: 8000000 INFO @ Tue, 16 Jun 2020 09:50:19: 3000000 INFO @ Tue, 16 Jun 2020 09:50:21: 13000000 INFO @ Tue, 16 Jun 2020 09:50:24: 9000000 INFO @ Tue, 16 Jun 2020 09:50:26: 4000000 INFO @ Tue, 16 Jun 2020 09:50:28: 14000000 INFO @ Tue, 16 Jun 2020 09:50:30: 10000000 INFO @ Tue, 16 Jun 2020 09:50:32: 5000000 INFO @ Tue, 16 Jun 2020 09:50:34: 15000000 INFO @ Tue, 16 Jun 2020 09:50:35: 11000000 INFO @ Tue, 16 Jun 2020 09:50:39: 6000000 INFO @ Tue, 16 Jun 2020 09:50:41: 16000000 INFO @ Tue, 16 Jun 2020 09:50:41: 12000000 INFO @ Tue, 16 Jun 2020 09:50:45: 7000000 INFO @ Tue, 16 Jun 2020 09:50:46: 13000000 INFO @ Tue, 16 Jun 2020 09:50:47: 17000000 INFO @ Tue, 16 Jun 2020 09:50:51: 8000000 INFO @ Tue, 16 Jun 2020 09:50:52: 14000000 INFO @ Tue, 16 Jun 2020 09:50:54: 18000000 INFO @ Tue, 16 Jun 2020 09:50:58: 15000000 INFO @ Tue, 16 Jun 2020 09:50:58: 9000000 INFO @ Tue, 16 Jun 2020 09:50:58: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:50:58: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:50:58: #1 total tags in treatment: 18762737 INFO @ Tue, 16 Jun 2020 09:50:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:50:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:50:59: #1 tags after filtering in treatment: 18762737 INFO @ Tue, 16 Jun 2020 09:50:59: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:50:59: #1 finished! INFO @ Tue, 16 Jun 2020 09:50:59: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:50:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:00: #2 number of paired peaks: 1389 INFO @ Tue, 16 Jun 2020 09:51:00: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:00: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:00: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:00: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:00: #2 predicted fragment length is 37 bps INFO @ Tue, 16 Jun 2020 09:51:00: #2 alternative fragment length(s) may be 3,37 bps INFO @ Tue, 16 Jun 2020 09:51:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.05_model.r WARNING @ Tue, 16 Jun 2020 09:51:00: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:51:00: #2 You may need to consider one of the other alternative d(s): 3,37 WARNING @ Tue, 16 Jun 2020 09:51:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:51:00: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:00: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:51:03: 16000000 INFO @ Tue, 16 Jun 2020 09:51:04: 10000000 INFO @ Tue, 16 Jun 2020 09:51:09: 17000000 INFO @ Tue, 16 Jun 2020 09:51:11: 11000000 INFO @ Tue, 16 Jun 2020 09:51:15: 18000000 INFO @ Tue, 16 Jun 2020 09:51:17: 12000000 INFO @ Tue, 16 Jun 2020 09:51:19: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:51:19: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:51:19: #1 total tags in treatment: 18762737 INFO @ Tue, 16 Jun 2020 09:51:19: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:51:19: #1 tags after filtering in treatment: 18762737 INFO @ Tue, 16 Jun 2020 09:51:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:19: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:19: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:51:21: #2 number of paired peaks: 1389 INFO @ Tue, 16 Jun 2020 09:51:21: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:21: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:21: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:21: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:21: #2 predicted fragment length is 37 bps INFO @ Tue, 16 Jun 2020 09:51:21: #2 alternative fragment length(s) may be 3,37 bps INFO @ Tue, 16 Jun 2020 09:51:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.10_model.r WARNING @ Tue, 16 Jun 2020 09:51:21: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:51:21: #2 You may need to consider one of the other alternative d(s): 3,37 WARNING @ Tue, 16 Jun 2020 09:51:21: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:51:21: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:21: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:51:23: 13000000 INFO @ Tue, 16 Jun 2020 09:51:29: 14000000 INFO @ Tue, 16 Jun 2020 09:51:33: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:51:35: 15000000 INFO @ Tue, 16 Jun 2020 09:51:41: 16000000 INFO @ Tue, 16 Jun 2020 09:51:47: 17000000 INFO @ Tue, 16 Jun 2020 09:51:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:51:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:51:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.05_summits.bed INFO @ Tue, 16 Jun 2020 09:51:50: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8941 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:51:53: 18000000 INFO @ Tue, 16 Jun 2020 09:51:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:51:58: #1 tag size is determined as 50 bps INFO @ Tue, 16 Jun 2020 09:51:58: #1 tag size = 50 INFO @ Tue, 16 Jun 2020 09:51:58: #1 total tags in treatment: 18762737 INFO @ Tue, 16 Jun 2020 09:51:58: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:51:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:51:58: #1 tags after filtering in treatment: 18762737 INFO @ Tue, 16 Jun 2020 09:51:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 16 Jun 2020 09:51:58: #1 finished! INFO @ Tue, 16 Jun 2020 09:51:58: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:51:58: #2 looking for paired plus/minus strand peaks... BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:51:59: #2 number of paired peaks: 1389 INFO @ Tue, 16 Jun 2020 09:51:59: start model_add_line... INFO @ Tue, 16 Jun 2020 09:51:59: start X-correlation... INFO @ Tue, 16 Jun 2020 09:51:59: end of X-cor INFO @ Tue, 16 Jun 2020 09:51:59: #2 finished! INFO @ Tue, 16 Jun 2020 09:51:59: #2 predicted fragment length is 37 bps INFO @ Tue, 16 Jun 2020 09:51:59: #2 alternative fragment length(s) may be 3,37 bps INFO @ Tue, 16 Jun 2020 09:51:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.20_model.r WARNING @ Tue, 16 Jun 2020 09:51:59: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:51:59: #2 You may need to consider one of the other alternative d(s): 3,37 WARNING @ Tue, 16 Jun 2020 09:51:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:51:59: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:51:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:52:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.10_summits.bed INFO @ Tue, 16 Jun 2020 09:52:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4102 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:52:30: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:52:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:52:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:52:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX5402752/SRX5402752.20_summits.bed INFO @ Tue, 16 Jun 2020 09:52:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (921 records, 4 fields): 2 millis CompletedMACS2peakCalling