Job ID = 14518003 SRX = SRX10533674 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2022-01-14T22:08:17 prefetch.2.10.7: 1) Downloading 'SRR14165397'... 2022-01-14T22:08:17 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:08:26 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:08:27 prefetch.2.10.7: 'SRR14165397' is valid 2022-01-14T22:08:27 prefetch.2.10.7: 1) 'SRR14165397' was downloaded successfully 2022-01-14T22:08:27 prefetch.2.10.7: 'SRR14165397' has 0 unresolved dependencies Read 4000000 spots for SRR14165397/SRR14165397.sra Written 4000000 spots for SRR14165397/SRR14165397.sra 2022-01-14T22:08:52 prefetch.2.10.7: 1) Downloading 'SRR14165398'... 2022-01-14T22:08:52 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:09:02 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:09:03 prefetch.2.10.7: 'SRR14165398' is valid 2022-01-14T22:09:03 prefetch.2.10.7: 1) 'SRR14165398' was downloaded successfully 2022-01-14T22:09:03 prefetch.2.10.7: 'SRR14165398' has 0 unresolved dependencies Read 4000000 spots for SRR14165398/SRR14165398.sra Written 4000000 spots for SRR14165398/SRR14165398.sra 2022-01-14T22:09:26 prefetch.2.10.7: 1) Downloading 'SRR14165399'... 2022-01-14T22:09:26 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:09:35 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:09:36 prefetch.2.10.7: 'SRR14165399' is valid 2022-01-14T22:09:36 prefetch.2.10.7: 1) 'SRR14165399' was downloaded successfully 2022-01-14T22:09:36 prefetch.2.10.7: 'SRR14165399' has 0 unresolved dependencies Read 4000000 spots for SRR14165399/SRR14165399.sra Written 4000000 spots for SRR14165399/SRR14165399.sra 2022-01-14T22:09:56 prefetch.2.10.7: 1) Downloading 'SRR14165400'... 2022-01-14T22:09:56 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:10:05 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:10:06 prefetch.2.10.7: 'SRR14165400' is valid 2022-01-14T22:10:06 prefetch.2.10.7: 1) 'SRR14165400' was downloaded successfully 2022-01-14T22:10:06 prefetch.2.10.7: 'SRR14165400' has 0 unresolved dependencies Read 4000000 spots for SRR14165400/SRR14165400.sra Written 4000000 spots for SRR14165400/SRR14165400.sra 2022-01-14T22:10:26 prefetch.2.10.7: 1) Downloading 'SRR14165401'... 2022-01-14T22:10:26 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:10:35 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:10:35 prefetch.2.10.7: 'SRR14165401' is valid 2022-01-14T22:10:35 prefetch.2.10.7: 1) 'SRR14165401' was downloaded successfully 2022-01-14T22:10:35 prefetch.2.10.7: 'SRR14165401' has 0 unresolved dependencies Read 4000000 spots for SRR14165401/SRR14165401.sra Written 4000000 spots for SRR14165401/SRR14165401.sra 2022-01-14T22:10:59 prefetch.2.10.7: 1) Downloading 'SRR14165402'... 2022-01-14T22:10:59 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:11:08 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:11:09 prefetch.2.10.7: 'SRR14165402' is valid 2022-01-14T22:11:09 prefetch.2.10.7: 1) 'SRR14165402' was downloaded successfully 2022-01-14T22:11:09 prefetch.2.10.7: 'SRR14165402' has 0 unresolved dependencies Read 4000000 spots for SRR14165402/SRR14165402.sra Written 4000000 spots for SRR14165402/SRR14165402.sra 2022-01-14T22:11:32 prefetch.2.10.7: 1) Downloading 'SRR14165403'... 2022-01-14T22:11:32 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:11:42 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:11:42 prefetch.2.10.7: 'SRR14165403' is valid 2022-01-14T22:11:42 prefetch.2.10.7: 1) 'SRR14165403' was downloaded successfully 2022-01-14T22:11:42 prefetch.2.10.7: 'SRR14165403' has 0 unresolved dependencies Read 4000000 spots for SRR14165403/SRR14165403.sra Written 4000000 spots for SRR14165403/SRR14165403.sra 2022-01-14T22:12:02 prefetch.2.10.7: 1) Downloading 'SRR14165404'... 2022-01-14T22:12:02 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:12:12 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:12:13 prefetch.2.10.7: 'SRR14165404' is valid 2022-01-14T22:12:13 prefetch.2.10.7: 1) 'SRR14165404' was downloaded successfully 2022-01-14T22:12:13 prefetch.2.10.7: 'SRR14165404' has 0 unresolved dependencies Read 4000000 spots for SRR14165404/SRR14165404.sra Written 4000000 spots for SRR14165404/SRR14165404.sra 2022-01-14T22:12:37 prefetch.2.10.7: 1) Downloading 'SRR14165405'... 2022-01-14T22:12:37 prefetch.2.10.7: Downloading via HTTPS... 2022-01-14T22:12:43 prefetch.2.10.7: HTTPS download succeed 2022-01-14T22:12:43 prefetch.2.10.7: 'SRR14165405' is valid 2022-01-14T22:12:43 prefetch.2.10.7: 1) 'SRR14165405' was downloaded successfully 2022-01-14T22:12:43 prefetch.2.10.7: 'SRR14165405' has 0 unresolved dependencies Read 2127602 spots for SRR14165405/SRR14165405.sra Written 2127602 spots for SRR14165405/SRR14165405.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: 00:10:30 34127602 reads; of these: 34127602 (100.00%) were unpaired; of these: 23411433 (68.60%) aligned 0 times 7952715 (23.30%) aligned exactly 1 time 2763454 (8.10%) aligned >1 times 31.40% overall alignment rate Time searching: 00:10:32 Overall time: 00:10:32 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] 4792312 / 10716169 = 0.4472 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 07:26:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.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 07:26:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 07:26:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 07:26:40: 1000000 INFO @ Sat, 15 Jan 2022 07:26:47: 2000000 INFO @ Sat, 15 Jan 2022 07:26:54: 3000000 INFO @ Sat, 15 Jan 2022 07:27:01: 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 07:27:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.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 07:27:03: #1 read tag files... INFO @ Sat, 15 Jan 2022 07:27:03: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 07:27:08: 5000000 INFO @ Sat, 15 Jan 2022 07:27:10: 1000000 INFO @ Sat, 15 Jan 2022 07:27:15: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 07:27:15: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 07:27:15: #1 total tags in treatment: 5923857 INFO @ Sat, 15 Jan 2022 07:27:15: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 07:27:15: #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 07:27:16: #1 tags after filtering in treatment: 5923592 INFO @ Sat, 15 Jan 2022 07:27:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 07:27:16: #1 finished! INFO @ Sat, 15 Jan 2022 07:27:16: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 07:27:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 07:27:17: #2 number of paired peaks: 11694 INFO @ Sat, 15 Jan 2022 07:27:17: start model_add_line... INFO @ Sat, 15 Jan 2022 07:27:17: start X-correlation... INFO @ Sat, 15 Jan 2022 07:27:17: end of X-cor INFO @ Sat, 15 Jan 2022 07:27:17: #2 finished! INFO @ Sat, 15 Jan 2022 07:27:17: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Jan 2022 07:27:17: #2 alternative fragment length(s) may be 51,242 bps INFO @ Sat, 15 Jan 2022 07:27:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.05_model.r WARNING @ Sat, 15 Jan 2022 07:27:17: #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 07:27:17: #2 You may need to consider one of the other alternative d(s): 51,242 WARNING @ Sat, 15 Jan 2022 07:27:17: #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 07:27:17: #3 Call peaks... INFO @ Sat, 15 Jan 2022 07:27:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 07:27:17: 2000000 INFO @ Sat, 15 Jan 2022 07:27:23: 3000000 INFO @ Sat, 15 Jan 2022 07:27:29: 4000000 INFO @ Sat, 15 Jan 2022 07:27:30: #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 07:27:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.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 07:27:33: #1 read tag files... INFO @ Sat, 15 Jan 2022 07:27:33: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 07:27:35: 5000000 INFO @ Sat, 15 Jan 2022 07:27:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.05_peaks.xls INFO @ Sat, 15 Jan 2022 07:27:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 07:27:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.05_summits.bed INFO @ Sat, 15 Jan 2022 07:27:37: Done! pass1 - making usageList (70 chroms): 1 millis pass2 - checking and writing primary data (946 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 07:27:40: 1000000 INFO @ Sat, 15 Jan 2022 07:27:41: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 07:27:41: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 07:27:41: #1 total tags in treatment: 5923857 INFO @ Sat, 15 Jan 2022 07:27:41: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 07:27:41: #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 07:27:42: #1 tags after filtering in treatment: 5923592 INFO @ Sat, 15 Jan 2022 07:27:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 07:27:42: #1 finished! INFO @ Sat, 15 Jan 2022 07:27:42: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 07:27:42: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 07:27:43: #2 number of paired peaks: 11694 INFO @ Sat, 15 Jan 2022 07:27:43: start model_add_line... INFO @ Sat, 15 Jan 2022 07:27:43: start X-correlation... INFO @ Sat, 15 Jan 2022 07:27:43: end of X-cor INFO @ Sat, 15 Jan 2022 07:27:43: #2 finished! INFO @ Sat, 15 Jan 2022 07:27:43: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Jan 2022 07:27:43: #2 alternative fragment length(s) may be 51,242 bps INFO @ Sat, 15 Jan 2022 07:27:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.10_model.r WARNING @ Sat, 15 Jan 2022 07:27:43: #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 07:27:43: #2 You may need to consider one of the other alternative d(s): 51,242 WARNING @ Sat, 15 Jan 2022 07:27:43: #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 07:27:43: #3 Call peaks... INFO @ Sat, 15 Jan 2022 07:27:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 07:27:47: 2000000 INFO @ Sat, 15 Jan 2022 07:27:53: 3000000 INFO @ Sat, 15 Jan 2022 07:27:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 07:27:59: 4000000 INFO @ Sat, 15 Jan 2022 07:28:02: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.10_peaks.xls INFO @ Sat, 15 Jan 2022 07:28:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 07:28:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.10_summits.bed INFO @ Sat, 15 Jan 2022 07:28:03: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (422 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 07:28:05: 5000000 INFO @ Sat, 15 Jan 2022 07:28:11: #1 tag size is determined as 51 bps INFO @ Sat, 15 Jan 2022 07:28:11: #1 tag size = 51 INFO @ Sat, 15 Jan 2022 07:28:11: #1 total tags in treatment: 5923857 INFO @ Sat, 15 Jan 2022 07:28:11: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 07:28:11: #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 07:28:11: #1 tags after filtering in treatment: 5923592 INFO @ Sat, 15 Jan 2022 07:28:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 07:28:11: #1 finished! INFO @ Sat, 15 Jan 2022 07:28:11: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 07:28:11: #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 07:28:13: #2 number of paired peaks: 11694 INFO @ Sat, 15 Jan 2022 07:28:13: start model_add_line... INFO @ Sat, 15 Jan 2022 07:28:13: start X-correlation... INFO @ Sat, 15 Jan 2022 07:28:13: end of X-cor INFO @ Sat, 15 Jan 2022 07:28:13: #2 finished! INFO @ Sat, 15 Jan 2022 07:28:13: #2 predicted fragment length is 51 bps INFO @ Sat, 15 Jan 2022 07:28:13: #2 alternative fragment length(s) may be 51,242 bps INFO @ Sat, 15 Jan 2022 07:28:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.20_model.r WARNING @ Sat, 15 Jan 2022 07:28:13: #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 07:28:13: #2 You may need to consider one of the other alternative d(s): 51,242 WARNING @ Sat, 15 Jan 2022 07:28:13: #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 07:28:13: #3 Call peaks... INFO @ Sat, 15 Jan 2022 07:28:13: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 07:28:26: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 07:28:33: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.20_peaks.xls INFO @ Sat, 15 Jan 2022 07:28:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 07:28:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX10533674/SRX10533674.20_summits.bed INFO @ Sat, 15 Jan 2022 07:28:33: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (138 records, 4 fields): 2 millis CompletedMACS2peakCalling