Job ID = 14518053 SRX = SRX10533694 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-01-14T23:04:49 prefetch.2.10.7: 1) Downloading 'SRR14165564'... 2022-01-14T23:04:49 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T23:05:00 prefetch.2.10.7: HTTPS download succeed 2022-01-14T23:05:00 prefetch.2.10.7: 'SRR14165564' is valid 2022-01-14T23:05:00 prefetch.2.10.7: 1) 'SRR14165564' was downloaded successfully 2022-01-14T23:05:00 prefetch.2.10.7: 'SRR14165564' has 0 unresolved dependencies Read 4000000 spots for SRR14165564/SRR14165564.sra Written 4000000 spots for SRR14165564/SRR14165564.sra 2022-01-14T23:05:21 prefetch.2.10.7: 1) Downloading 'SRR14165565'... 2022-01-14T23:05:21 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T23:05:35 prefetch.2.10.7: HTTPS download succeed 2022-01-14T23:05:36 prefetch.2.10.7: 'SRR14165565' is valid 2022-01-14T23:05:36 prefetch.2.10.7: 1) 'SRR14165565' was downloaded successfully 2022-01-14T23:05:36 prefetch.2.10.7: 'SRR14165565' has 0 unresolved dependencies Read 4000000 spots for SRR14165565/SRR14165565.sra Written 4000000 spots for SRR14165565/SRR14165565.sra 2022-01-14T23:06:00 prefetch.2.10.7: 1) Downloading 'SRR14165566'... 2022-01-14T23:06:00 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T23:06:10 prefetch.2.10.7: HTTPS download succeed 2022-01-14T23:06:10 prefetch.2.10.7: 'SRR14165566' is valid 2022-01-14T23:06:10 prefetch.2.10.7: 1) 'SRR14165566' was downloaded successfully 2022-01-14T23:06:10 prefetch.2.10.7: 'SRR14165566' has 0 unresolved dependencies Read 4000000 spots for SRR14165566/SRR14165566.sra Written 4000000 spots for SRR14165566/SRR14165566.sra 2022-01-14T23:06:31 prefetch.2.10.7: 1) Downloading 'SRR14165567'... 2022-01-14T23:06:31 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T23:06:42 prefetch.2.10.7: HTTPS download succeed 2022-01-14T23:06:42 prefetch.2.10.7: 'SRR14165567' is valid 2022-01-14T23:06:42 prefetch.2.10.7: 1) 'SRR14165567' was downloaded successfully 2022-01-14T23:06:42 prefetch.2.10.7: 'SRR14165567' has 0 unresolved dependencies Read 4000000 spots for SRR14165567/SRR14165567.sra Written 4000000 spots for SRR14165567/SRR14165567.sra Read 4000000 spots for SRR14165568/SRR14165568.sra Written 4000000 spots for SRR14165568/SRR14165568.sra Read 4000000 spots for SRR14165569/SRR14165569.sra Written 4000000 spots for SRR14165569/SRR14165569.sra 2022-01-14T23:07:36 prefetch.2.10.7: 1) Downloading 'SRR14165570'... 2022-01-14T23:07:36 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T23:07:46 prefetch.2.10.7: HTTPS download succeed 2022-01-14T23:07:47 prefetch.2.10.7: 'SRR14165570' is valid 2022-01-14T23:07:47 prefetch.2.10.7: 1) 'SRR14165570' was downloaded successfully 2022-01-14T23:07:47 prefetch.2.10.7: 'SRR14165570' has 0 unresolved dependencies Read 4000000 spots for SRR14165570/SRR14165570.sra Written 4000000 spots for SRR14165570/SRR14165570.sra Read 120384 spots for SRR14165571/SRR14165571.sra Written 120384 spots for SRR14165571/SRR14165571.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:11:53 28120384 reads; of these: 28120384 (100.00%) were unpaired; of these: 10680323 (37.98%) aligned 0 times 13086641 (46.54%) aligned exactly 1 time 4353420 (15.48%) aligned >1 times 62.02% overall alignment rate Time searching: 00:11:56 Overall time: 00:11:56 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] 1153927 / 17440061 = 0.0662 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 08:25:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.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 08:25:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 08:25:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 08:25:14: 1000000 INFO @ Sat, 15 Jan 2022 08:25:20: 2000000 INFO @ Sat, 15 Jan 2022 08:25:25: 3000000 INFO @ Sat, 15 Jan 2022 08:25:31: 4000000 INFO @ Sat, 15 Jan 2022 08:25:36: 5000000 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 08:25:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.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 08:25:39: #1 read tag files... INFO @ Sat, 15 Jan 2022 08:25:39: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 08:25:42: 6000000 INFO @ Sat, 15 Jan 2022 08:25:45: 1000000 INFO @ Sat, 15 Jan 2022 08:25:48: 7000000 INFO @ Sat, 15 Jan 2022 08:25:53: 2000000 INFO @ Sat, 15 Jan 2022 08:25:55: 8000000 INFO @ Sat, 15 Jan 2022 08:25:59: 3000000 INFO @ Sat, 15 Jan 2022 08:26:01: 9000000 INFO @ Sat, 15 Jan 2022 08:26:06: 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 08:26:07: 10000000 INFO @ Sat, 15 Jan 2022 08:26:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.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 08:26:09: #1 read tag files... INFO @ Sat, 15 Jan 2022 08:26:09: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 08:26:13: 5000000 INFO @ Sat, 15 Jan 2022 08:26:13: 11000000 INFO @ Sat, 15 Jan 2022 08:26:16: 1000000 INFO @ Sat, 15 Jan 2022 08:26:20: 12000000 INFO @ Sat, 15 Jan 2022 08:26:20: 6000000 INFO @ Sat, 15 Jan 2022 08:26:22: 2000000 INFO @ Sat, 15 Jan 2022 08:26:26: 13000000 INFO @ Sat, 15 Jan 2022 08:26:27: 7000000 INFO @ Sat, 15 Jan 2022 08:26:28: 3000000 INFO @ Sat, 15 Jan 2022 08:26:32: 14000000 INFO @ Sat, 15 Jan 2022 08:26:33: 8000000 INFO @ Sat, 15 Jan 2022 08:26:35: 4000000 INFO @ Sat, 15 Jan 2022 08:26:39: 15000000 INFO @ Sat, 15 Jan 2022 08:26:40: 9000000 INFO @ Sat, 15 Jan 2022 08:26:41: 5000000 INFO @ Sat, 15 Jan 2022 08:26:45: 16000000 INFO @ Sat, 15 Jan 2022 08:26:47: 10000000 INFO @ Sat, 15 Jan 2022 08:26:47: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 08:26:47: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 08:26:47: #1 total tags in treatment: 16286134 INFO @ Sat, 15 Jan 2022 08:26:47: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 08:26:47: #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 08:26:47: 6000000 INFO @ Sat, 15 Jan 2022 08:26:47: #1 tags after filtering in treatment: 16285943 INFO @ Sat, 15 Jan 2022 08:26:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 08:26:47: #1 finished! INFO @ Sat, 15 Jan 2022 08:26:47: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 08:26:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 08:26:49: #2 number of paired peaks: 5625 INFO @ Sat, 15 Jan 2022 08:26:49: start model_add_line... INFO @ Sat, 15 Jan 2022 08:26:49: start X-correlation... INFO @ Sat, 15 Jan 2022 08:26:49: end of X-cor INFO @ Sat, 15 Jan 2022 08:26:49: #2 finished! INFO @ Sat, 15 Jan 2022 08:26:49: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Jan 2022 08:26:49: #2 alternative fragment length(s) may be 51,173 bps INFO @ Sat, 15 Jan 2022 08:26:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.05_model.r WARNING @ Sat, 15 Jan 2022 08:26:49: #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 08:26:49: #2 You may need to consider one of the other alternative d(s): 51,173 WARNING @ Sat, 15 Jan 2022 08:26:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Jan 2022 08:26:49: #3 Call peaks... INFO @ Sat, 15 Jan 2022 08:26:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 08:26:53: 7000000 INFO @ Sat, 15 Jan 2022 08:26:54: 11000000 INFO @ Sat, 15 Jan 2022 08:27:00: 8000000 INFO @ Sat, 15 Jan 2022 08:27:00: 12000000 INFO @ Sat, 15 Jan 2022 08:27:06: 9000000 INFO @ Sat, 15 Jan 2022 08:27:07: 13000000 INFO @ Sat, 15 Jan 2022 08:27:12: 10000000 INFO @ Sat, 15 Jan 2022 08:27:14: 14000000 INFO @ Sat, 15 Jan 2022 08:27:18: 11000000 INFO @ Sat, 15 Jan 2022 08:27:21: 15000000 INFO @ Sat, 15 Jan 2022 08:27:24: 12000000 INFO @ Sat, 15 Jan 2022 08:27:25: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 08:27:27: 16000000 INFO @ Sat, 15 Jan 2022 08:27:29: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 08:27:29: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 08:27:29: #1 total tags in treatment: 16286134 INFO @ Sat, 15 Jan 2022 08:27:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 08:27:29: #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 08:27:30: #1 tags after filtering in treatment: 16285943 INFO @ Sat, 15 Jan 2022 08:27:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 08:27:30: #1 finished! INFO @ Sat, 15 Jan 2022 08:27:30: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 08:27:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 08:27:30: 13000000 INFO @ Sat, 15 Jan 2022 08:27:31: #2 number of paired peaks: 5625 INFO @ Sat, 15 Jan 2022 08:27:31: start model_add_line... INFO @ Sat, 15 Jan 2022 08:27:31: start X-correlation... INFO @ Sat, 15 Jan 2022 08:27:31: end of X-cor INFO @ Sat, 15 Jan 2022 08:27:31: #2 finished! INFO @ Sat, 15 Jan 2022 08:27:31: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Jan 2022 08:27:31: #2 alternative fragment length(s) may be 51,173 bps INFO @ Sat, 15 Jan 2022 08:27:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.10_model.r WARNING @ Sat, 15 Jan 2022 08:27:31: #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 08:27:31: #2 You may need to consider one of the other alternative d(s): 51,173 WARNING @ Sat, 15 Jan 2022 08:27:31: #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 08:27:31: #3 Call peaks... INFO @ Sat, 15 Jan 2022 08:27:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 08:27:36: 14000000 INFO @ Sat, 15 Jan 2022 08:27:42: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 08:27:43: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.05_peaks.xls INFO @ Sat, 15 Jan 2022 08:27:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 08:27:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.05_summits.bed INFO @ Sat, 15 Jan 2022 08:27:43: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (1295 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 08:27:48: 16000000 INFO @ Sat, 15 Jan 2022 08:27:49: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 08:27:49: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 08:27:49: #1 total tags in treatment: 16286134 INFO @ Sat, 15 Jan 2022 08:27:49: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 08:27:49: #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 08:27:50: #1 tags after filtering in treatment: 16285943 INFO @ Sat, 15 Jan 2022 08:27:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 08:27:50: #1 finished! INFO @ Sat, 15 Jan 2022 08:27:50: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 08:27:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 08:27:51: #2 number of paired peaks: 5625 INFO @ Sat, 15 Jan 2022 08:27:51: start model_add_line... INFO @ Sat, 15 Jan 2022 08:27:51: start X-correlation... INFO @ Sat, 15 Jan 2022 08:27:51: end of X-cor INFO @ Sat, 15 Jan 2022 08:27:51: #2 finished! INFO @ Sat, 15 Jan 2022 08:27:51: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Jan 2022 08:27:51: #2 alternative fragment length(s) may be 51,173 bps INFO @ Sat, 15 Jan 2022 08:27:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.20_model.r WARNING @ Sat, 15 Jan 2022 08:27:51: #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 08:27:51: #2 You may need to consider one of the other alternative d(s): 51,173 WARNING @ Sat, 15 Jan 2022 08:27:51: #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 08:27:51: #3 Call peaks... INFO @ Sat, 15 Jan 2022 08:27:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 08:28:07: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 08:28:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.10_peaks.xls INFO @ Sat, 15 Jan 2022 08:28:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 08:28:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.10_summits.bed INFO @ Sat, 15 Jan 2022 08:28:24: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (658 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 08:28:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 08:28:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.20_peaks.xls INFO @ Sat, 15 Jan 2022 08:28:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 08:28:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533694/SRX10533694.20_summits.bed INFO @ Sat, 15 Jan 2022 08:28:44: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (269 records, 4 fields): 16 millis CompletedMACS2peakCalling