Job ID = 14517897 SRX = SRX6581765 Genome = rn6 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... Read 24156527 spots for SRR9825039/SRR9825039.sra Written 24156527 spots for SRR9825039/SRR9825039.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: 00:50:34 24156527 reads; of these: 24156527 (100.00%) were unpaired; of these: 669608 (2.77%) aligned 0 times 17015998 (70.44%) aligned exactly 1 time 6470921 (26.79%) aligned >1 times 97.23% overall alignment rate Time searching: 00:50:36 Overall time: 00:50:36 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] 1769597 / 23486919 = 0.0753 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 07:05:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.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 07:05:19: #1 read tag files... INFO @ Sat, 15 Jan 2022 07:05:19: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 07:05:30: 1000000 INFO @ Sat, 15 Jan 2022 07:05:41: 2000000 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 07:05:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.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 07:05:48: #1 read tag files... INFO @ Sat, 15 Jan 2022 07:05:48: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 07:05:52: 3000000 INFO @ Sat, 15 Jan 2022 07:06:00: 1000000 INFO @ Sat, 15 Jan 2022 07:06:04: 4000000 INFO @ Sat, 15 Jan 2022 07:06:11: 2000000 INFO @ Sat, 15 Jan 2022 07:06:15: 5000000 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 07:06:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.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 07:06:18: #1 read tag files... INFO @ Sat, 15 Jan 2022 07:06:18: #1 read treatment tags... INFO @ Sat, 15 Jan 2022 07:06:23: 3000000 INFO @ Sat, 15 Jan 2022 07:06:27: 6000000 INFO @ Sat, 15 Jan 2022 07:06:28: 1000000 INFO @ Sat, 15 Jan 2022 07:06:34: 4000000 INFO @ Sat, 15 Jan 2022 07:06:38: 2000000 INFO @ Sat, 15 Jan 2022 07:06:39: 7000000 INFO @ Sat, 15 Jan 2022 07:06:46: 5000000 INFO @ Sat, 15 Jan 2022 07:06:48: 3000000 INFO @ Sat, 15 Jan 2022 07:06:50: 8000000 INFO @ Sat, 15 Jan 2022 07:06:58: 4000000 INFO @ Sat, 15 Jan 2022 07:06:59: 6000000 INFO @ Sat, 15 Jan 2022 07:07:02: 9000000 INFO @ Sat, 15 Jan 2022 07:07:08: 5000000 INFO @ Sat, 15 Jan 2022 07:07:11: 7000000 INFO @ Sat, 15 Jan 2022 07:07:13: 10000000 INFO @ Sat, 15 Jan 2022 07:07:19: 6000000 INFO @ Sat, 15 Jan 2022 07:07:24: 8000000 INFO @ Sat, 15 Jan 2022 07:07:24: 11000000 INFO @ Sat, 15 Jan 2022 07:07:29: 7000000 INFO @ Sat, 15 Jan 2022 07:07:36: 12000000 INFO @ Sat, 15 Jan 2022 07:07:36: 9000000 INFO @ Sat, 15 Jan 2022 07:07:39: 8000000 INFO @ Sat, 15 Jan 2022 07:07:47: 13000000 INFO @ Sat, 15 Jan 2022 07:07:49: 9000000 INFO @ Sat, 15 Jan 2022 07:07:49: 10000000 INFO @ Sat, 15 Jan 2022 07:07:59: 10000000 INFO @ Sat, 15 Jan 2022 07:07:59: 14000000 INFO @ Sat, 15 Jan 2022 07:08:01: 11000000 INFO @ Sat, 15 Jan 2022 07:08:08: 11000000 INFO @ Sat, 15 Jan 2022 07:08:11: 15000000 INFO @ Sat, 15 Jan 2022 07:08:13: 12000000 INFO @ Sat, 15 Jan 2022 07:08:18: 12000000 INFO @ Sat, 15 Jan 2022 07:08:22: 16000000 INFO @ Sat, 15 Jan 2022 07:08:24: 13000000 INFO @ Sat, 15 Jan 2022 07:08:28: 13000000 INFO @ Sat, 15 Jan 2022 07:08:34: 17000000 INFO @ Sat, 15 Jan 2022 07:08:35: 14000000 INFO @ Sat, 15 Jan 2022 07:08:38: 14000000 INFO @ Sat, 15 Jan 2022 07:08:45: 18000000 INFO @ Sat, 15 Jan 2022 07:08:47: 15000000 INFO @ Sat, 15 Jan 2022 07:08:48: 15000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 15 Jan 2022 07:08:57: 19000000 INFO @ Sat, 15 Jan 2022 07:08:58: 16000000 INFO @ Sat, 15 Jan 2022 07:08:59: 16000000 INFO @ Sat, 15 Jan 2022 07:09:08: 17000000 INFO @ Sat, 15 Jan 2022 07:09:08: 20000000 INFO @ Sat, 15 Jan 2022 07:09:10: 17000000 INFO @ Sat, 15 Jan 2022 07:09:17: 18000000 INFO @ Sat, 15 Jan 2022 07:09:20: 21000000 INFO @ Sat, 15 Jan 2022 07:09:22: 18000000 INFO @ Sat, 15 Jan 2022 07:09:27: 19000000 INFO @ Sat, 15 Jan 2022 07:09:29: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 07:09:29: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 07:09:29: #1 total tags in treatment: 21717322 INFO @ Sat, 15 Jan 2022 07:09:29: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 07:09:29: #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 07:09:30: #1 tags after filtering in treatment: 21717193 INFO @ Sat, 15 Jan 2022 07:09:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 07:09:30: #1 finished! INFO @ Sat, 15 Jan 2022 07:09:30: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 07:09:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 07:09:33: #2 number of paired peaks: 4818 INFO @ Sat, 15 Jan 2022 07:09:33: start model_add_line... INFO @ Sat, 15 Jan 2022 07:09:33: start X-correlation... INFO @ Sat, 15 Jan 2022 07:09:33: end of X-cor INFO @ Sat, 15 Jan 2022 07:09:33: #2 finished! INFO @ Sat, 15 Jan 2022 07:09:33: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 07:09:33: #2 alternative fragment length(s) may be 75,547 bps INFO @ Sat, 15 Jan 2022 07:09:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.05_model.r WARNING @ Sat, 15 Jan 2022 07:09:33: #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 07:09:33: #2 You may need to consider one of the other alternative d(s): 75,547 WARNING @ Sat, 15 Jan 2022 07:09:33: #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 07:09:33: #3 Call peaks... INFO @ Sat, 15 Jan 2022 07:09:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 07:09:34: 19000000 INFO @ Sat, 15 Jan 2022 07:09:37: 20000000 INFO @ Sat, 15 Jan 2022 07:09:45: 20000000 INFO @ Sat, 15 Jan 2022 07:09:47: 21000000 INFO @ Sat, 15 Jan 2022 07:09:54: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 07:09:54: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 07:09:54: #1 total tags in treatment: 21717322 INFO @ Sat, 15 Jan 2022 07:09:54: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 07:09:54: #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 07:09:54: #1 tags after filtering in treatment: 21717193 INFO @ Sat, 15 Jan 2022 07:09:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 07:09:54: #1 finished! INFO @ Sat, 15 Jan 2022 07:09:54: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 07:09:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 07:09:57: 21000000 INFO @ Sat, 15 Jan 2022 07:09:57: #2 number of paired peaks: 4818 INFO @ Sat, 15 Jan 2022 07:09:57: start model_add_line... INFO @ Sat, 15 Jan 2022 07:09:57: start X-correlation... INFO @ Sat, 15 Jan 2022 07:09:57: end of X-cor INFO @ Sat, 15 Jan 2022 07:09:57: #2 finished! INFO @ Sat, 15 Jan 2022 07:09:57: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 07:09:57: #2 alternative fragment length(s) may be 75,547 bps INFO @ Sat, 15 Jan 2022 07:09:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.20_model.r WARNING @ Sat, 15 Jan 2022 07:09:57: #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 07:09:57: #2 You may need to consider one of the other alternative d(s): 75,547 WARNING @ Sat, 15 Jan 2022 07:09:57: #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 07:09:57: #3 Call peaks... INFO @ Sat, 15 Jan 2022 07:09:57: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 15 Jan 2022 07:10:05: #1 tag size is determined as 75 bps INFO @ Sat, 15 Jan 2022 07:10:05: #1 tag size = 75 INFO @ Sat, 15 Jan 2022 07:10:05: #1 total tags in treatment: 21717322 INFO @ Sat, 15 Jan 2022 07:10:05: #1 user defined the maximum tags... INFO @ Sat, 15 Jan 2022 07:10:05: #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 07:10:06: #1 tags after filtering in treatment: 21717193 INFO @ Sat, 15 Jan 2022 07:10:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Jan 2022 07:10:06: #1 finished! INFO @ Sat, 15 Jan 2022 07:10:06: #2 Build Peak Model... INFO @ Sat, 15 Jan 2022 07:10:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Jan 2022 07:10:08: #2 number of paired peaks: 4818 INFO @ Sat, 15 Jan 2022 07:10:08: start model_add_line... INFO @ Sat, 15 Jan 2022 07:10:09: start X-correlation... INFO @ Sat, 15 Jan 2022 07:10:09: end of X-cor INFO @ Sat, 15 Jan 2022 07:10:09: #2 finished! INFO @ Sat, 15 Jan 2022 07:10:09: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Jan 2022 07:10:09: #2 alternative fragment length(s) may be 75,547 bps INFO @ Sat, 15 Jan 2022 07:10:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.10_model.r WARNING @ Sat, 15 Jan 2022 07:10:09: #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 07:10:09: #2 You may need to consider one of the other alternative d(s): 75,547 WARNING @ Sat, 15 Jan 2022 07:10:09: #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 07:10:09: #3 Call peaks... INFO @ Sat, 15 Jan 2022 07:10:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Jan 2022 07:10:41: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 07:11:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 07:11:18: #3 Call peaks for each chromosome... INFO @ Sat, 15 Jan 2022 07:11:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.05_peaks.xls INFO @ Sat, 15 Jan 2022 07:11:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.05_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 07:11:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.05_summits.bed INFO @ Sat, 15 Jan 2022 07:11:19: Done! pass1 - making usageList (50 chroms): 2 millis pass2 - checking and writing primary data (1328 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 07:11:42: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.20_peaks.xls INFO @ Sat, 15 Jan 2022 07:11:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.20_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 07:11:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.20_summits.bed INFO @ Sat, 15 Jan 2022 07:11:42: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (436 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Jan 2022 07:11:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.10_peaks.xls INFO @ Sat, 15 Jan 2022 07:11:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.10_peaks.narrowPeak INFO @ Sat, 15 Jan 2022 07:11:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX6581765/SRX6581765.10_summits.bed INFO @ Sat, 15 Jan 2022 07:11:56: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (796 records, 4 fields): 19 millis CompletedMACS2peakCalling