Job ID = 12531441 SRX = SRX3087666 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 20972218 spots for SRR5927302/SRR5927302.sra Written 20972218 spots for SRR5927302/SRR5927302.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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:26:15 20972218 reads; of these: 20972218 (100.00%) were unpaired; of these: 2174290 (10.37%) aligned 0 times 13900509 (66.28%) aligned exactly 1 time 4897419 (23.35%) aligned >1 times 89.63% overall alignment rate Time searching: 00:26:19 Overall time: 00:26:20 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3916313 / 18797928 = 0.2083 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 07:57:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 17 Apr 2021 07:57:50: #1 read tag files... INFO @ Sat, 17 Apr 2021 07:57:50: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 07:57:57: 1000000 INFO @ Sat, 17 Apr 2021 07:58:04: 2000000 INFO @ Sat, 17 Apr 2021 07:58:12: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 07:58:19: 4000000 INFO @ Sat, 17 Apr 2021 07:58:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 17 Apr 2021 07:58:20: #1 read tag files... INFO @ Sat, 17 Apr 2021 07:58:20: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 07:58:27: 5000000 INFO @ Sat, 17 Apr 2021 07:58:28: 1000000 INFO @ Sat, 17 Apr 2021 07:58:35: 6000000 INFO @ Sat, 17 Apr 2021 07:58:35: 2000000 INFO @ Sat, 17 Apr 2021 07:58:43: 7000000 INFO @ Sat, 17 Apr 2021 07:58:43: 3000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 17 Apr 2021 07:58:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 17 Apr 2021 07:58:50: #1 read tag files... INFO @ Sat, 17 Apr 2021 07:58:50: #1 read treatment tags... INFO @ Sat, 17 Apr 2021 07:58:51: 8000000 INFO @ Sat, 17 Apr 2021 07:58:51: 4000000 INFO @ Sat, 17 Apr 2021 07:58:58: 1000000 INFO @ Sat, 17 Apr 2021 07:58:59: 5000000 INFO @ Sat, 17 Apr 2021 07:58:59: 9000000 INFO @ Sat, 17 Apr 2021 07:59:05: 2000000 INFO @ Sat, 17 Apr 2021 07:59:06: 6000000 INFO @ Sat, 17 Apr 2021 07:59:07: 10000000 INFO @ Sat, 17 Apr 2021 07:59:13: 3000000 INFO @ Sat, 17 Apr 2021 07:59:14: 7000000 INFO @ Sat, 17 Apr 2021 07:59:15: 11000000 INFO @ Sat, 17 Apr 2021 07:59:20: 4000000 INFO @ Sat, 17 Apr 2021 07:59:21: 8000000 INFO @ Sat, 17 Apr 2021 07:59:23: 12000000 INFO @ Sat, 17 Apr 2021 07:59:28: 5000000 INFO @ Sat, 17 Apr 2021 07:59:29: 9000000 INFO @ Sat, 17 Apr 2021 07:59:31: 13000000 INFO @ Sat, 17 Apr 2021 07:59:35: 6000000 INFO @ Sat, 17 Apr 2021 07:59:36: 10000000 INFO @ Sat, 17 Apr 2021 07:59:39: 14000000 INFO @ Sat, 17 Apr 2021 07:59:43: 7000000 INFO @ Sat, 17 Apr 2021 07:59:44: 11000000 INFO @ Sat, 17 Apr 2021 07:59:47: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 07:59:47: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 07:59:47: #1 total tags in treatment: 14881615 INFO @ Sat, 17 Apr 2021 07:59:47: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 07:59:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 07:59:47: #1 tags after filtering in treatment: 14881435 INFO @ Sat, 17 Apr 2021 07:59:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 07:59:47: #1 finished! INFO @ Sat, 17 Apr 2021 07:59:47: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 07:59:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 07:59:49: #2 number of paired peaks: 21208 INFO @ Sat, 17 Apr 2021 07:59:49: start model_add_line... INFO @ Sat, 17 Apr 2021 07:59:49: start X-correlation... INFO @ Sat, 17 Apr 2021 07:59:49: end of X-cor INFO @ Sat, 17 Apr 2021 07:59:49: #2 finished! INFO @ Sat, 17 Apr 2021 07:59:49: #2 predicted fragment length is 85 bps INFO @ Sat, 17 Apr 2021 07:59:49: #2 alternative fragment length(s) may be 85 bps INFO @ Sat, 17 Apr 2021 07:59:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.05_model.r WARNING @ Sat, 17 Apr 2021 07:59:49: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 07:59:49: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Sat, 17 Apr 2021 07:59:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 07:59:49: #3 Call peaks... INFO @ Sat, 17 Apr 2021 07:59:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 07:59:50: 8000000 INFO @ Sat, 17 Apr 2021 07:59:51: 12000000 INFO @ Sat, 17 Apr 2021 07:59:57: 9000000 INFO @ Sat, 17 Apr 2021 07:59:58: 13000000 INFO @ Sat, 17 Apr 2021 08:00:05: 10000000 INFO @ Sat, 17 Apr 2021 08:00:05: 14000000 INFO @ Sat, 17 Apr 2021 08:00:12: 11000000 INFO @ Sat, 17 Apr 2021 08:00:12: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 08:00:12: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 08:00:12: #1 total tags in treatment: 14881615 INFO @ Sat, 17 Apr 2021 08:00:12: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:00:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 08:00:12: #1 tags after filtering in treatment: 14881435 INFO @ Sat, 17 Apr 2021 08:00:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 08:00:12: #1 finished! INFO @ Sat, 17 Apr 2021 08:00:12: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:00:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:00:15: #2 number of paired peaks: 21208 INFO @ Sat, 17 Apr 2021 08:00:15: start model_add_line... INFO @ Sat, 17 Apr 2021 08:00:15: start X-correlation... INFO @ Sat, 17 Apr 2021 08:00:15: end of X-cor INFO @ Sat, 17 Apr 2021 08:00:15: #2 finished! INFO @ Sat, 17 Apr 2021 08:00:15: #2 predicted fragment length is 85 bps INFO @ Sat, 17 Apr 2021 08:00:15: #2 alternative fragment length(s) may be 85 bps INFO @ Sat, 17 Apr 2021 08:00:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.10_model.r WARNING @ Sat, 17 Apr 2021 08:00:15: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:00:15: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Sat, 17 Apr 2021 08:00:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:00:15: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:00:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:00:18: 12000000 INFO @ Sat, 17 Apr 2021 08:00:25: 13000000 INFO @ Sat, 17 Apr 2021 08:00:27: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:00:32: 14000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 17 Apr 2021 08:00:37: #1 tag size is determined as 61 bps INFO @ Sat, 17 Apr 2021 08:00:37: #1 tag size = 61 INFO @ Sat, 17 Apr 2021 08:00:37: #1 total tags in treatment: 14881615 INFO @ Sat, 17 Apr 2021 08:00:37: #1 user defined the maximum tags... INFO @ Sat, 17 Apr 2021 08:00:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 17 Apr 2021 08:00:38: #1 tags after filtering in treatment: 14881435 INFO @ Sat, 17 Apr 2021 08:00:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 17 Apr 2021 08:00:38: #1 finished! INFO @ Sat, 17 Apr 2021 08:00:38: #2 Build Peak Model... INFO @ Sat, 17 Apr 2021 08:00:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 17 Apr 2021 08:00:40: #2 number of paired peaks: 21208 INFO @ Sat, 17 Apr 2021 08:00:40: start model_add_line... INFO @ Sat, 17 Apr 2021 08:00:40: start X-correlation... INFO @ Sat, 17 Apr 2021 08:00:40: end of X-cor INFO @ Sat, 17 Apr 2021 08:00:40: #2 finished! INFO @ Sat, 17 Apr 2021 08:00:40: #2 predicted fragment length is 85 bps INFO @ Sat, 17 Apr 2021 08:00:40: #2 alternative fragment length(s) may be 85 bps INFO @ Sat, 17 Apr 2021 08:00:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.20_model.r WARNING @ Sat, 17 Apr 2021 08:00:40: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 17 Apr 2021 08:00:40: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Sat, 17 Apr 2021 08:00:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 17 Apr 2021 08:00:40: #3 Call peaks... INFO @ Sat, 17 Apr 2021 08:00:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 17 Apr 2021 08:00:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.05_peaks.xls INFO @ Sat, 17 Apr 2021 08:00:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.05_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:00:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.05_summits.bed INFO @ Sat, 17 Apr 2021 08:00:47: Done! pass1 - making usageList (61 chroms): 1 millis pass2 - checking and writing primary data (6264 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:00:56: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 17 Apr 2021 08:01:17: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.10_peaks.xls INFO @ Sat, 17 Apr 2021 08:01:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.10_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:01:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.10_summits.bed INFO @ Sat, 17 Apr 2021 08:01:17: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (1954 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 17 Apr 2021 08:01:19: #3 Call peaks for each chromosome... INFO @ Sat, 17 Apr 2021 08:01:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.20_peaks.xls INFO @ Sat, 17 Apr 2021 08:01:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.20_peaks.narrowPeak INFO @ Sat, 17 Apr 2021 08:01:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX3087666/SRX3087666.20_summits.bed INFO @ Sat, 17 Apr 2021 08:01:39: Done! pass1 - making usageList (27 chroms): 1 millis pass2 - checking and writing primary data (232 records, 4 fields): 2 millis CompletedMACS2peakCalling