Job ID = 14160596 SRX = SRX9567191 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:25:04 13413645 reads; of these: 13413645 (100.00%) were paired; of these: 6054304 (45.14%) aligned concordantly 0 times 6535754 (48.72%) aligned concordantly exactly 1 time 823587 (6.14%) aligned concordantly >1 times ---- 6054304 pairs aligned concordantly 0 times; of these: 4487629 (74.12%) aligned discordantly 1 time ---- 1566675 pairs aligned 0 times concordantly or discordantly; of these: 3133350 mates make up the pairs; of these: 1317311 (42.04%) aligned 0 times 841822 (26.87%) aligned exactly 1 time 974217 (31.09%) aligned >1 times 95.09% overall alignment rate Time searching: 00:25:04 Overall time: 00:25:04 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 20 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] 8698748 / 11842086 = 0.7346 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 @ Thu, 09 Dec 2021 03:52:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 09 Dec 2021 03:52:45: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:52:45: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:52:51: 1000000 INFO @ Thu, 09 Dec 2021 03:52:58: 2000000 INFO @ Thu, 09 Dec 2021 03:53:04: 3000000 INFO @ Thu, 09 Dec 2021 03:53:11: 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 @ Thu, 09 Dec 2021 03:53:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 09 Dec 2021 03:53:15: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:53:15: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:53:18: 5000000 INFO @ Thu, 09 Dec 2021 03:53:22: 1000000 INFO @ Thu, 09 Dec 2021 03:53:25: 6000000 INFO @ Thu, 09 Dec 2021 03:53:30: 2000000 INFO @ Thu, 09 Dec 2021 03:53:33: 7000000 INFO @ Thu, 09 Dec 2021 03:53:37: 3000000 INFO @ Thu, 09 Dec 2021 03:53:40: 8000000 INFO @ Thu, 09 Dec 2021 03:53:41: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:53:41: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:53:41: #1 total tags in treatment: 1961917 INFO @ Thu, 09 Dec 2021 03:53:41: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:53:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:53:41: #1 tags after filtering in treatment: 1847570 INFO @ Thu, 09 Dec 2021 03:53:41: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 09 Dec 2021 03:53:41: #1 finished! INFO @ Thu, 09 Dec 2021 03:53:41: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:53:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:53:41: #2 number of paired peaks: 2046 INFO @ Thu, 09 Dec 2021 03:53:41: start model_add_line... INFO @ Thu, 09 Dec 2021 03:53:41: start X-correlation... INFO @ Thu, 09 Dec 2021 03:53:41: end of X-cor INFO @ Thu, 09 Dec 2021 03:53:41: #2 finished! INFO @ Thu, 09 Dec 2021 03:53:41: #2 predicted fragment length is 276 bps INFO @ Thu, 09 Dec 2021 03:53:41: #2 alternative fragment length(s) may be 276 bps INFO @ Thu, 09 Dec 2021 03:53:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.05_model.r WARNING @ Thu, 09 Dec 2021 03:53:41: #2 Since the d (276) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:53:41: #2 You may need to consider one of the other alternative d(s): 276 WARNING @ Thu, 09 Dec 2021 03:53:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:53:41: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:53:41: #3 Pre-compute pvalue-qvalue table... 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 @ Thu, 09 Dec 2021 03:53:44: 4000000 INFO @ Thu, 09 Dec 2021 03:53:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 09 Dec 2021 03:53:45: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:53:45: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:53:46: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:53:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:53:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:53:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.05_summits.bed INFO @ Thu, 09 Dec 2021 03:53:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1417 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:53:52: 5000000 INFO @ Thu, 09 Dec 2021 03:53:54: 1000000 INFO @ Thu, 09 Dec 2021 03:54:00: 6000000 INFO @ Thu, 09 Dec 2021 03:54:04: 2000000 INFO @ Thu, 09 Dec 2021 03:54:08: 7000000 INFO @ Thu, 09 Dec 2021 03:54:14: 3000000 INFO @ Thu, 09 Dec 2021 03:54:16: 8000000 INFO @ Thu, 09 Dec 2021 03:54:17: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:54:17: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:54:17: #1 total tags in treatment: 1961917 INFO @ Thu, 09 Dec 2021 03:54:17: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:54:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:54:17: #1 tags after filtering in treatment: 1847570 INFO @ Thu, 09 Dec 2021 03:54:17: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 09 Dec 2021 03:54:17: #1 finished! INFO @ Thu, 09 Dec 2021 03:54:17: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:54:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:54:17: #2 number of paired peaks: 2046 INFO @ Thu, 09 Dec 2021 03:54:17: start model_add_line... INFO @ Thu, 09 Dec 2021 03:54:17: start X-correlation... INFO @ Thu, 09 Dec 2021 03:54:17: end of X-cor INFO @ Thu, 09 Dec 2021 03:54:17: #2 finished! INFO @ Thu, 09 Dec 2021 03:54:17: #2 predicted fragment length is 276 bps INFO @ Thu, 09 Dec 2021 03:54:17: #2 alternative fragment length(s) may be 276 bps INFO @ Thu, 09 Dec 2021 03:54:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.10_model.r WARNING @ Thu, 09 Dec 2021 03:54:17: #2 Since the d (276) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:54:17: #2 You may need to consider one of the other alternative d(s): 276 WARNING @ Thu, 09 Dec 2021 03:54:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:54:17: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:54:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:54:22: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:54:23: 4000000 INFO @ Thu, 09 Dec 2021 03:54:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:54:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:54:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.10_summits.bed INFO @ Thu, 09 Dec 2021 03:54:24: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (682 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:54:32: 5000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:54:41: 6000000 INFO @ Thu, 09 Dec 2021 03:54:50: 7000000 INFO @ Thu, 09 Dec 2021 03:54:59: 8000000 INFO @ Thu, 09 Dec 2021 03:55:00: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:55:00: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:55:00: #1 total tags in treatment: 1961917 INFO @ Thu, 09 Dec 2021 03:55:00: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:55:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:55:00: #1 tags after filtering in treatment: 1847570 INFO @ Thu, 09 Dec 2021 03:55:00: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 09 Dec 2021 03:55:00: #1 finished! INFO @ Thu, 09 Dec 2021 03:55:00: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:55:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:55:01: #2 number of paired peaks: 2046 INFO @ Thu, 09 Dec 2021 03:55:01: start model_add_line... INFO @ Thu, 09 Dec 2021 03:55:01: start X-correlation... INFO @ Thu, 09 Dec 2021 03:55:01: end of X-cor INFO @ Thu, 09 Dec 2021 03:55:01: #2 finished! INFO @ Thu, 09 Dec 2021 03:55:01: #2 predicted fragment length is 276 bps INFO @ Thu, 09 Dec 2021 03:55:01: #2 alternative fragment length(s) may be 276 bps INFO @ Thu, 09 Dec 2021 03:55:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.20_model.r WARNING @ Thu, 09 Dec 2021 03:55:01: #2 Since the d (276) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:55:01: #2 You may need to consider one of the other alternative d(s): 276 WARNING @ Thu, 09 Dec 2021 03:55:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:55:01: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:55:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:55:05: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:55:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:55:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:55:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX9567191/SRX9567191.20_summits.bed INFO @ Thu, 09 Dec 2021 03:55:07: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (327 records, 4 fields): 9 millis CompletedMACS2peakCalling