Job ID = 14518017 SRX = SRX10533675 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-01-14T22:28:57 prefetch.2.10.7: 1) Downloading 'SRR14165406'... 2022-01-14T22:28:57 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:29:10 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:29:10 prefetch.2.10.7: 'SRR14165406' is valid 2022-01-14T22:29:10 prefetch.2.10.7: 1) 'SRR14165406' was downloaded successfully 2022-01-14T22:29:10 prefetch.2.10.7: 'SRR14165406' has 0 unresolved dependencies Read 4000000 spots for SRR14165406/SRR14165406.sra Written 4000000 spots for SRR14165406/SRR14165406.sra 2022-01-14T22:29:32 prefetch.2.10.7: 1) Downloading 'SRR14165407'... 2022-01-14T22:29:32 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:29:41 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:29:41 prefetch.2.10.7: 'SRR14165407' is valid 2022-01-14T22:29:41 prefetch.2.10.7: 1) 'SRR14165407' was downloaded successfully 2022-01-14T22:29:41 prefetch.2.10.7: 'SRR14165407' has 0 unresolved dependencies Read 4000000 spots for SRR14165407/SRR14165407.sra Written 4000000 spots for SRR14165407/SRR14165407.sra 2022-01-14T22:30:06 prefetch.2.10.7: 1) Downloading 'SRR14165408'... 2022-01-14T22:30:06 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:30:16 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:30:17 prefetch.2.10.7: 'SRR14165408' is valid 2022-01-14T22:30:17 prefetch.2.10.7: 1) 'SRR14165408' was downloaded successfully 2022-01-14T22:30:17 prefetch.2.10.7: 'SRR14165408' has 0 unresolved dependencies Read 4000000 spots for SRR14165408/SRR14165408.sra Written 4000000 spots for SRR14165408/SRR14165408.sra Read 4000000 spots for SRR14165409/SRR14165409.sra Written 4000000 spots for SRR14165409/SRR14165409.sra Read 4000000 spots for SRR14165410/SRR14165410.sra Written 4000000 spots for SRR14165410/SRR14165410.sra Read 4000000 spots for SRR14165411/SRR14165411.sra Written 4000000 spots for SRR14165411/SRR14165411.sra Read 4000000 spots for SRR14165412/SRR14165412.sra Written 4000000 spots for SRR14165412/SRR14165412.sra Read 4000000 spots for SRR14165413/SRR14165413.sra Written 4000000 spots for SRR14165413/SRR14165413.sra Read 2107950 spots for SRR14165414/SRR14165414.sra Written 2107950 spots for SRR14165414/SRR14165414.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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:12:56 34107950 reads; of these: 34107950 (100.00%) were unpaired; of these: 23899509 (70.07%) aligned 0 times 7233074 (21.21%) aligned exactly 1 time 2975367 (8.72%) aligned >1 times 29.93% overall alignment rate Time searching: 00:12:58 Overall time: 00:12:58 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] 3520843 / 10208441 = 0.3449 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 07:48:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.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 07:48:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 07:48:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 07:48:24: 1000000 INFO @ Sat, 15 Jan 2022 07:48:30: 2000000 INFO @ Sat, 15 Jan 2022 07:48:36: 3000000 INFO @ Sat, 15 Jan 2022 07:48:42: 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 07:48:48: 5000000 INFO @ Sat, 15 Jan 2022 07:48:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.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 07:48:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 07:48:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 07:48:55: 6000000 INFO @ Sat, 15 Jan 2022 07:48:56: 1000000 INFO @ Sat, 15 Jan 2022 07:48:59: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 07:48:59: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 07:48:59: #1 total tags in treatment: 6687598 INFO @ Sat, 15 Jan 2022 07:48:59: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 07:48:59: #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 07:49:00: #1 tags after filtering in treatment: 6687358 INFO @ Sat, 15 Jan 2022 07:49:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 07:49:00: #1 finished! INFO @ Sat, 15 Jan 2022 07:49:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 07:49:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 07:49:01: #2 number of paired peaks: 7891 INFO @ Sat, 15 Jan 2022 07:49:01: start model_add_line... INFO @ Sat, 15 Jan 2022 07:49:01: start X-correlation... INFO @ Sat, 15 Jan 2022 07:49:01: end of X-cor INFO @ Sat, 15 Jan 2022 07:49:01: #2 finished! INFO @ Sat, 15 Jan 2022 07:49:01: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 07:49:01: #2 alternative fragment length(s) may be 50,159,187,230 bps INFO @ Sat, 15 Jan 2022 07:49:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.05_model.r WARNING @ Sat, 15 Jan 2022 07:49:01: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 07:49:01: #2 You may need to consider one of the other alternative d(s): 50,159,187,230 WARNING @ Sat, 15 Jan 2022 07:49:01: #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 07:49:01: #3 Call peaks... INFO @ Sat, 15 Jan 2022 07:49:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 07:49:03: 2000000 INFO @ Sat, 15 Jan 2022 07:49:11: 3000000 INFO @ Sat, 15 Jan 2022 07:49:15: #3 Call peaks for each chromosome... 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 07:49:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.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 07:49:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 07:49:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 07:49:19: 4000000 INFO @ Sat, 15 Jan 2022 07:49:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.05_peaks.xls INFO @ Sat, 15 Jan 2022 07:49:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 07:49:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.05_summits.bed INFO @ Sat, 15 Jan 2022 07:49:22: Done! pass1 - making usageList (78 chroms): 0 millis pass2 - checking and writing primary data (1379 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 07:49:26: 1000000 INFO @ Sat, 15 Jan 2022 07:49:27: 5000000 INFO @ Sat, 15 Jan 2022 07:49:33: 2000000 INFO @ Sat, 15 Jan 2022 07:49:36: 6000000 INFO @ Sat, 15 Jan 2022 07:49:40: 3000000 INFO @ Sat, 15 Jan 2022 07:49:42: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 07:49:42: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 07:49:42: #1 total tags in treatment: 6687598 INFO @ Sat, 15 Jan 2022 07:49:42: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 07:49:42: #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 07:49:42: #1 tags after filtering in treatment: 6687358 INFO @ Sat, 15 Jan 2022 07:49:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 07:49:42: #1 finished! INFO @ Sat, 15 Jan 2022 07:49:42: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 07:49:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 07:49:43: #2 number of paired peaks: 7891 INFO @ Sat, 15 Jan 2022 07:49:43: start model_add_line... INFO @ Sat, 15 Jan 2022 07:49:43: start X-correlation... INFO @ Sat, 15 Jan 2022 07:49:43: end of X-cor INFO @ Sat, 15 Jan 2022 07:49:43: #2 finished! INFO @ Sat, 15 Jan 2022 07:49:43: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 07:49:43: #2 alternative fragment length(s) may be 50,159,187,230 bps INFO @ Sat, 15 Jan 2022 07:49:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.10_model.r WARNING @ Sat, 15 Jan 2022 07:49:43: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 07:49:43: #2 You may need to consider one of the other alternative d(s): 50,159,187,230 WARNING @ Sat, 15 Jan 2022 07:49:43: #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 07:49:43: #3 Call peaks... INFO @ Sat, 15 Jan 2022 07:49:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 07:49:47: 4000000 INFO @ Sat, 15 Jan 2022 07:49:53: 5000000 INFO @ Sat, 15 Jan 2022 07:49:59: 6000000 INFO @ Sat, 15 Jan 2022 07:49:59: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 07:50:03: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 07:50:03: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 07:50:03: #1 total tags in treatment: 6687598 INFO @ Sat, 15 Jan 2022 07:50:03: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 07:50:03: #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 07:50:03: #1 tags after filtering in treatment: 6687358 INFO @ Sat, 15 Jan 2022 07:50:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 07:50:03: #1 finished! INFO @ Sat, 15 Jan 2022 07:50:03: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 07:50:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 07:50:04: #2 number of paired peaks: 7891 INFO @ Sat, 15 Jan 2022 07:50:04: start model_add_line... INFO @ Sat, 15 Jan 2022 07:50:04: start X-correlation... INFO @ Sat, 15 Jan 2022 07:50:04: end of X-cor INFO @ Sat, 15 Jan 2022 07:50:04: #2 finished! INFO @ Sat, 15 Jan 2022 07:50:04: #2 predicted fragment length is 50 bps INFO @ Sat, 15 Jan 2022 07:50:04: #2 alternative fragment length(s) may be 50,159,187,230 bps INFO @ Sat, 15 Jan 2022 07:50:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.20_model.r WARNING @ Sat, 15 Jan 2022 07:50:04: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 07:50:04: #2 You may need to consider one of the other alternative d(s): 50,159,187,230 WARNING @ Sat, 15 Jan 2022 07:50:04: #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 07:50:04: #3 Call peaks... INFO @ Sat, 15 Jan 2022 07:50:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 07:50:06: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.10_peaks.xls INFO @ Sat, 15 Jan 2022 07:50:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 07:50:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.10_summits.bed INFO @ Sat, 15 Jan 2022 07:50:06: Done! pass1 - making usageList (62 chroms): 1 millis pass2 - checking and writing primary data (654 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 07:50:19: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 07:50:26: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.20_peaks.xls INFO @ Sat, 15 Jan 2022 07:50:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 07:50:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533675/SRX10533675.20_summits.bed INFO @ Sat, 15 Jan 2022 07:50:26: Done! pass1 - making usageList (49 chroms): 1 millis pass2 - checking and writing primary data (264 records, 4 fields): 3 millis CompletedMACS2peakCalling