Job ID = 14518046 SRX = SRX10533689 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 4000000 spots for SRR14165516/SRR14165516.sra Written 4000000 spots for SRR14165516/SRR14165516.sra 2022-01-14T22:54:26 prefetch.2.10.7: 1) Downloading 'SRR14165517'... 2022-01-14T22:54:26 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:54:36 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:54:36 prefetch.2.10.7: 'SRR14165517' is valid 2022-01-14T22:54:36 prefetch.2.10.7: 1) 'SRR14165517' was downloaded successfully 2022-01-14T22:54:36 prefetch.2.10.7: 'SRR14165517' has 0 unresolved dependencies Read 4000000 spots for SRR14165517/SRR14165517.sra Written 4000000 spots for SRR14165517/SRR14165517.sra Read 4000000 spots for SRR14165518/SRR14165518.sra Written 4000000 spots for SRR14165518/SRR14165518.sra Read 4000000 spots for SRR14165519/SRR14165519.sra Written 4000000 spots for SRR14165519/SRR14165519.sra Read 4000000 spots for SRR14165520/SRR14165520.sra Written 4000000 spots for SRR14165520/SRR14165520.sra Read 4000000 spots for SRR14165521/SRR14165521.sra Written 4000000 spots for SRR14165521/SRR14165521.sra Read 4000000 spots for SRR14165522/SRR14165522.sra Written 4000000 spots for SRR14165522/SRR14165522.sra Read 4000000 spots for SRR14165523/SRR14165523.sra Written 4000000 spots for SRR14165523/SRR14165523.sra Read 487146 spots for SRR14165524/SRR14165524.sra Written 487146 spots for SRR14165524/SRR14165524.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: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:06 32487146 reads; of these: 32487146 (100.00%) were unpaired; of these: 11686279 (35.97%) aligned 0 times 15066158 (46.38%) aligned exactly 1 time 5734709 (17.65%) aligned >1 times 64.03% overall alignment rate Time searching: 00:14:08 Overall time: 00:14:08 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 12 files... [bam_rmdupse_core] 3872431 / 20800867 = 0.1862 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/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 08:16:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.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, 15 Jan 2022 08:16:56: #1 read tag files... INFO @ Sat, 15 Jan 2022 08:16:56: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 08:17:01: 1000000 INFO @ Sat, 15 Jan 2022 08:17:07: 2000000 INFO @ Sat, 15 Jan 2022 08:17:13: 3000000 INFO @ Sat, 15 Jan 2022 08:17:19: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 08:17:24: 5000000 INFO @ Sat, 15 Jan 2022 08:17:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.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, 15 Jan 2022 08:17:25: #1 read tag files... INFO @ Sat, 15 Jan 2022 08:17:25: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 08:17:31: 6000000 INFO @ Sat, 15 Jan 2022 08:17:32: 1000000 INFO @ Sat, 15 Jan 2022 08:17:37: 7000000 INFO @ Sat, 15 Jan 2022 08:17:39: 2000000 INFO @ Sat, 15 Jan 2022 08:17:44: 8000000 INFO @ Sat, 15 Jan 2022 08:17:45: 3000000 INFO @ Sat, 15 Jan 2022 08:17:50: 9000000 INFO @ Sat, 15 Jan 2022 08:17:51: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.8.3/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 15 Jan 2022 08:17:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.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, 15 Jan 2022 08:17:55: #1 read tag files... INFO @ Sat, 15 Jan 2022 08:17:55: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 08:17:57: 10000000 INFO @ Sat, 15 Jan 2022 08:17:58: 5000000 INFO @ Sat, 15 Jan 2022 08:18:03: 1000000 INFO @ Sat, 15 Jan 2022 08:18:04: 11000000 INFO @ Sat, 15 Jan 2022 08:18:05: 6000000 INFO @ Sat, 15 Jan 2022 08:18:10: 2000000 INFO @ Sat, 15 Jan 2022 08:18:10: 12000000 INFO @ Sat, 15 Jan 2022 08:18:12: 7000000 INFO @ Sat, 15 Jan 2022 08:18:17: 3000000 INFO @ Sat, 15 Jan 2022 08:18:17: 13000000 INFO @ Sat, 15 Jan 2022 08:18:19: 8000000 INFO @ Sat, 15 Jan 2022 08:18:24: 14000000 INFO @ Sat, 15 Jan 2022 08:18:25: 4000000 INFO @ Sat, 15 Jan 2022 08:18:26: 9000000 INFO @ Sat, 15 Jan 2022 08:18:31: 15000000 INFO @ Sat, 15 Jan 2022 08:18:32: 5000000 INFO @ Sat, 15 Jan 2022 08:18:33: 10000000 INFO @ Sat, 15 Jan 2022 08:18:38: 16000000 INFO @ Sat, 15 Jan 2022 08:18:39: 6000000 INFO @ Sat, 15 Jan 2022 08:18:39: 11000000 INFO @ Sat, 15 Jan 2022 08:18:45: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 08:18:45: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 08:18:45: #1 total tags in treatment: 16928436 INFO @ Sat, 15 Jan 2022 08:18:45: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 08:18:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 08:18:45: #1 tags after filtering in treatment: 16928279 INFO @ Sat, 15 Jan 2022 08:18:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 08:18:45: #1 finished! INFO @ Sat, 15 Jan 2022 08:18:45: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 08:18:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 08:18:46: 12000000 INFO @ Sat, 15 Jan 2022 08:18:46: #2 number of paired peaks: 5896 INFO @ Sat, 15 Jan 2022 08:18:46: start model_add_line... INFO @ Sat, 15 Jan 2022 08:18:47: 7000000 INFO @ Sat, 15 Jan 2022 08:18:47: start X-correlation... INFO @ Sat, 15 Jan 2022 08:18:47: end of X-cor INFO @ Sat, 15 Jan 2022 08:18:47: #2 finished! INFO @ Sat, 15 Jan 2022 08:18:47: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Jan 2022 08:18:47: #2 alternative fragment length(s) may be 51,157,196 bps INFO @ Sat, 15 Jan 2022 08:18:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.05_model.r WARNING @ Sat, 15 Jan 2022 08:18:47: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 08:18:47: #2 You may need to consider one of the other alternative d(s): 51,157,196 WARNING @ Sat, 15 Jan 2022 08:18:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 08:18:47: #3 Call peaks... INFO @ Sat, 15 Jan 2022 08:18:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 08:18:53: 13000000 INFO @ Sat, 15 Jan 2022 08:18:54: 8000000 INFO @ Sat, 15 Jan 2022 08:19:00: 14000000 INFO @ Sat, 15 Jan 2022 08:19:01: 9000000 INFO @ Sat, 15 Jan 2022 08:19:07: 15000000 INFO @ Sat, 15 Jan 2022 08:19:08: 10000000 INFO @ Sat, 15 Jan 2022 08:19:14: 16000000 INFO @ Sat, 15 Jan 2022 08:19:16: 11000000 INFO @ Sat, 15 Jan 2022 08:19:21: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 08:19:21: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 08:19:21: #1 total tags in treatment: 16928436 INFO @ Sat, 15 Jan 2022 08:19:21: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 08:19:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 08:19:21: #1 tags after filtering in treatment: 16928279 INFO @ Sat, 15 Jan 2022 08:19:21: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 08:19:21: #1 finished! INFO @ Sat, 15 Jan 2022 08:19:21: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 08:19:21: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 08:19:23: #2 number of paired peaks: 5896 INFO @ Sat, 15 Jan 2022 08:19:23: start model_add_line... INFO @ Sat, 15 Jan 2022 08:19:23: start X-correlation... INFO @ Sat, 15 Jan 2022 08:19:23: end of X-cor INFO @ Sat, 15 Jan 2022 08:19:23: #2 finished! INFO @ Sat, 15 Jan 2022 08:19:23: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Jan 2022 08:19:23: #2 alternative fragment length(s) may be 51,157,196 bps INFO @ Sat, 15 Jan 2022 08:19:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.10_model.r WARNING @ Sat, 15 Jan 2022 08:19:23: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 08:19:23: #2 You may need to consider one of the other alternative d(s): 51,157,196 WARNING @ Sat, 15 Jan 2022 08:19:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 08:19:23: #3 Call peaks... INFO @ Sat, 15 Jan 2022 08:19:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 08:19:23: 12000000 INFO @ Sat, 15 Jan 2022 08:19:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 08:19:30: 13000000 INFO @ Sat, 15 Jan 2022 08:19:37: 14000000 INFO @ Sat, 15 Jan 2022 08:19:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.05_peaks.xls INFO @ Sat, 15 Jan 2022 08:19:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 08:19:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.05_summits.bed INFO @ Sat, 15 Jan 2022 08:19:42: Done! pass1 - making usageList (55 chroms): 1 millis pass2 - checking and writing primary data (1561 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 08:19:44: 15000000 INFO @ Sat, 15 Jan 2022 08:19:50: 16000000 BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 08:19:57: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 08:19:57: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 08:19:57: #1 total tags in treatment: 16928436 INFO @ Sat, 15 Jan 2022 08:19:57: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 08:19:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Jan 2022 08:19:57: #1 tags after filtering in treatment: 16928279 INFO @ Sat, 15 Jan 2022 08:19:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 08:19:57: #1 finished! INFO @ Sat, 15 Jan 2022 08:19:57: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 08:19:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 08:19:59: #2 number of paired peaks: 5896 INFO @ Sat, 15 Jan 2022 08:19:59: start model_add_line... INFO @ Sat, 15 Jan 2022 08:19:59: start X-correlation... INFO @ Sat, 15 Jan 2022 08:19:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 08:19:59: end of X-cor INFO @ Sat, 15 Jan 2022 08:19:59: #2 finished! INFO @ Sat, 15 Jan 2022 08:19:59: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Jan 2022 08:19:59: #2 alternative fragment length(s) may be 51,157,196 bps INFO @ Sat, 15 Jan 2022 08:19:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.20_model.r WARNING @ Sat, 15 Jan 2022 08:19:59: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 08:19:59: #2 You may need to consider one of the other alternative d(s): 51,157,196 WARNING @ Sat, 15 Jan 2022 08:19:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 08:19:59: #3 Call peaks... INFO @ Sat, 15 Jan 2022 08:19:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 08:20:17: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.10_peaks.xls INFO @ Sat, 15 Jan 2022 08:20:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 08:20:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.10_summits.bed INFO @ Sat, 15 Jan 2022 08:20:17: Done! pass1 - making usageList (46 chroms): 0 millis pass2 - checking and writing primary data (864 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 08:20:35: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 08:20:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.20_peaks.xls INFO @ Sat, 15 Jan 2022 08:20:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 08:20:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533689/SRX10533689.20_summits.bed INFO @ Sat, 15 Jan 2022 08:20:54: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (379 records, 4 fields): 2 millis CompletedMACS2peakCalling