Job ID = 14519594 SRX = SRX6581708 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 11841695 spots for SRR9825033/SRR9825033.sra Written 11841695 spots for SRR9825033/SRR9825033.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: 00:16:13 11841695 reads; of these: 11841695 (100.00%) were unpaired; of these: 286741 (2.42%) aligned 0 times 8544939 (72.16%) aligned exactly 1 time 3010015 (25.42%) aligned >1 times 97.58% overall alignment rate Time searching: 00:16:17 Overall time: 00:16:17 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] 707759 / 11554954 = 0.0613 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 16:48:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.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 16:48:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 16:48:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 16:48:51: 1000000 INFO @ Sat, 15 Jan 2022 16:48:58: 2000000 INFO @ Sat, 15 Jan 2022 16:49:04: 3000000 INFO @ Sat, 15 Jan 2022 16:49:11: 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 16:49:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.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 16:49:15: #1 read tag files... INFO @ Sat, 15 Jan 2022 16:49:15: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 16:49:18: 5000000 INFO @ Sat, 15 Jan 2022 16:49:22: 1000000 INFO @ Sat, 15 Jan 2022 16:49:25: 6000000 INFO @ Sat, 15 Jan 2022 16:49:29: 2000000 INFO @ Sat, 15 Jan 2022 16:49:32: 7000000 INFO @ Sat, 15 Jan 2022 16:49:36: 3000000 INFO @ Sat, 15 Jan 2022 16:49:39: 8000000 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 16:49:43: 4000000 INFO @ Sat, 15 Jan 2022 16:49:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.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 16:49:45: #1 read tag files... INFO @ Sat, 15 Jan 2022 16:49:45: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 16:49:46: 9000000 INFO @ Sat, 15 Jan 2022 16:49:51: 5000000 INFO @ Sat, 15 Jan 2022 16:49:52: 1000000 INFO @ Sat, 15 Jan 2022 16:49:54: 10000000 INFO @ Sat, 15 Jan 2022 16:49:58: 6000000 INFO @ Sat, 15 Jan 2022 16:50:00: 2000000 INFO @ Sat, 15 Jan 2022 16:50:00: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 16:50:00: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 16:50:00: #1 total tags in treatment: 10847195 INFO @ Sat, 15 Jan 2022 16:50:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 16:50:00: #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 16:50:01: #1 tags after filtering in treatment: 10846976 INFO @ Sat, 15 Jan 2022 16:50:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 16:50:01: #1 finished! INFO @ Sat, 15 Jan 2022 16:50:01: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 16:50:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 16:50:02: #2 number of paired peaks: 4549 INFO @ Sat, 15 Jan 2022 16:50:02: start model_add_line... INFO @ Sat, 15 Jan 2022 16:50:02: start X-correlation... INFO @ Sat, 15 Jan 2022 16:50:02: end of X-cor INFO @ Sat, 15 Jan 2022 16:50:02: #2 finished! INFO @ Sat, 15 Jan 2022 16:50:02: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 16:50:02: #2 alternative fragment length(s) may be 75,247,543 bps INFO @ Sat, 15 Jan 2022 16:50:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.05_model.r WARNING @ Sat, 15 Jan 2022 16:50:02: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 16:50:02: #2 You may need to consider one of the other alternative d(s): 75,247,543 WARNING @ Sat, 15 Jan 2022 16:50:02: #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 16:50:02: #3 Call peaks... INFO @ Sat, 15 Jan 2022 16:50:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 16:50:05: 7000000 INFO @ Sat, 15 Jan 2022 16:50:07: 3000000 INFO @ Sat, 15 Jan 2022 16:50:12: 8000000 INFO @ Sat, 15 Jan 2022 16:50:14: 4000000 INFO @ Sat, 15 Jan 2022 16:50:18: 9000000 INFO @ Sat, 15 Jan 2022 16:50:21: 5000000 INFO @ Sat, 15 Jan 2022 16:50:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 16:50:25: 10000000 INFO @ Sat, 15 Jan 2022 16:50:27: 6000000 INFO @ Sat, 15 Jan 2022 16:50:32: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 16:50:32: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 16:50:32: #1 total tags in treatment: 10847195 INFO @ Sat, 15 Jan 2022 16:50:32: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 16:50:32: #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 16:50:32: #1 tags after filtering in treatment: 10846976 INFO @ Sat, 15 Jan 2022 16:50:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 16:50:32: #1 finished! INFO @ Sat, 15 Jan 2022 16:50:32: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 16:50:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 16:50:34: #2 number of paired peaks: 4549 INFO @ Sat, 15 Jan 2022 16:50:34: start model_add_line... INFO @ Sat, 15 Jan 2022 16:50:34: start X-correlation... INFO @ Sat, 15 Jan 2022 16:50:34: end of X-cor INFO @ Sat, 15 Jan 2022 16:50:34: #2 finished! INFO @ Sat, 15 Jan 2022 16:50:34: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 16:50:34: #2 alternative fragment length(s) may be 75,247,543 bps INFO @ Sat, 15 Jan 2022 16:50:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.10_model.r WARNING @ Sat, 15 Jan 2022 16:50:34: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 16:50:34: #2 You may need to consider one of the other alternative d(s): 75,247,543 WARNING @ Sat, 15 Jan 2022 16:50:34: #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 16:50:34: #3 Call peaks... INFO @ Sat, 15 Jan 2022 16:50:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 16:50:34: 7000000 INFO @ Sat, 15 Jan 2022 16:50:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.05_peaks.xls INFO @ Sat, 15 Jan 2022 16:50:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 16:50:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.05_summits.bed INFO @ Sat, 15 Jan 2022 16:50:37: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (764 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 16:50:41: 8000000 INFO @ Sat, 15 Jan 2022 16:50:47: 9000000 INFO @ Sat, 15 Jan 2022 16:50:54: 10000000 INFO @ Sat, 15 Jan 2022 16:50:56: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 16:51:00: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 16:51:00: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 16:51:00: #1 total tags in treatment: 10847195 INFO @ Sat, 15 Jan 2022 16:51:00: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 16:51:00: #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 16:51:00: #1 tags after filtering in treatment: 10846976 INFO @ Sat, 15 Jan 2022 16:51:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 16:51:00: #1 finished! INFO @ Sat, 15 Jan 2022 16:51:00: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 16:51:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 16:51:01: #2 number of paired peaks: 4549 INFO @ Sat, 15 Jan 2022 16:51:01: start model_add_line... INFO @ Sat, 15 Jan 2022 16:51:02: start X-correlation... INFO @ Sat, 15 Jan 2022 16:51:02: end of X-cor INFO @ Sat, 15 Jan 2022 16:51:02: #2 finished! INFO @ Sat, 15 Jan 2022 16:51:02: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 16:51:02: #2 alternative fragment length(s) may be 75,247,543 bps INFO @ Sat, 15 Jan 2022 16:51:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.20_model.r WARNING @ Sat, 15 Jan 2022 16:51:02: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Jan 2022 16:51:02: #2 You may need to consider one of the other alternative d(s): 75,247,543 WARNING @ Sat, 15 Jan 2022 16:51:02: #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 16:51:02: #3 Call peaks... INFO @ Sat, 15 Jan 2022 16:51:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 16:51:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.10_peaks.xls INFO @ Sat, 15 Jan 2022 16:51:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 16:51:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.10_summits.bed INFO @ Sat, 15 Jan 2022 16:51:09: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (461 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 16:51:24: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 16:51:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.20_peaks.xls INFO @ Sat, 15 Jan 2022 16:51:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 16:51:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581708/SRX6581708.20_summits.bed INFO @ Sat, 15 Jan 2022 16:51:37: Done! pass1 - making usageList (24 chroms): 1 millis pass2 - checking and writing primary data (258 records, 4 fields): 21 millis CompletedMACS2peakCalling BigWig に変換しました。