Job ID = 14159111 SRX = SRX10641188 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: 00:22:31 19320360 reads; of these: 19320360 (100.00%) were paired; of these: 12691932 (65.69%) aligned concordantly 0 times 5907017 (30.57%) aligned concordantly exactly 1 time 721411 (3.73%) aligned concordantly >1 times ---- 12691932 pairs aligned concordantly 0 times; of these: 2055715 (16.20%) aligned discordantly 1 time ---- 10636217 pairs aligned 0 times concordantly or discordantly; of these: 21272434 mates make up the pairs; of these: 20414533 (95.97%) aligned 0 times 486256 (2.29%) aligned exactly 1 time 371645 (1.75%) aligned >1 times 47.17% overall alignment rate Time searching: 00:22:31 Overall time: 00:22:31 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 16 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] 1321057 / 8646977 = 0.1528 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 @ Wed, 08 Dec 2021 20:07:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.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 @ Wed, 08 Dec 2021 20:07:12: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:07:12: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:07:20: 1000000 INFO @ Wed, 08 Dec 2021 20:07:29: 2000000 INFO @ Wed, 08 Dec 2021 20:07:40: 3000000 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 @ Wed, 08 Dec 2021 20:07:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.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 @ Wed, 08 Dec 2021 20:07:42: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:07:42: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:07:52: 4000000 INFO @ Wed, 08 Dec 2021 20:07:53: 1000000 INFO @ Wed, 08 Dec 2021 20:08:04: 2000000 INFO @ Wed, 08 Dec 2021 20:08:05: 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 @ Wed, 08 Dec 2021 20:08:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.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 @ Wed, 08 Dec 2021 20:08:12: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:08:12: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:08:15: 3000000 INFO @ Wed, 08 Dec 2021 20:08:18: 6000000 INFO @ Wed, 08 Dec 2021 20:08:25: 1000000 INFO @ Wed, 08 Dec 2021 20:08:27: 4000000 INFO @ Wed, 08 Dec 2021 20:08:30: 7000000 INFO @ Wed, 08 Dec 2021 20:08:37: 2000000 INFO @ Wed, 08 Dec 2021 20:08:38: 5000000 INFO @ Wed, 08 Dec 2021 20:08:43: 8000000 INFO @ Wed, 08 Dec 2021 20:08:49: 3000000 INFO @ Wed, 08 Dec 2021 20:08:50: 6000000 INFO @ Wed, 08 Dec 2021 20:08:56: 9000000 INFO @ Wed, 08 Dec 2021 20:09:01: 7000000 INFO @ Wed, 08 Dec 2021 20:09:02: 4000000 INFO @ Wed, 08 Dec 2021 20:09:09: 10000000 INFO @ Wed, 08 Dec 2021 20:09:12: 8000000 INFO @ Wed, 08 Dec 2021 20:09:14: 5000000 INFO @ Wed, 08 Dec 2021 20:09:22: 11000000 INFO @ Wed, 08 Dec 2021 20:09:24: 9000000 INFO @ Wed, 08 Dec 2021 20:09:26: 6000000 INFO @ Wed, 08 Dec 2021 20:09:35: 12000000 INFO @ Wed, 08 Dec 2021 20:09:35: 10000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:09:39: 7000000 INFO @ Wed, 08 Dec 2021 20:09:47: 11000000 INFO @ Wed, 08 Dec 2021 20:09:48: 13000000 INFO @ Wed, 08 Dec 2021 20:09:51: 8000000 INFO @ Wed, 08 Dec 2021 20:09:58: 12000000 INFO @ Wed, 08 Dec 2021 20:10:01: 14000000 INFO @ Wed, 08 Dec 2021 20:10:03: 9000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:10:09: 13000000 INFO @ Wed, 08 Dec 2021 20:10:12: 15000000 INFO @ Wed, 08 Dec 2021 20:10:15: 10000000 INFO @ Wed, 08 Dec 2021 20:10:18: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 20:10:18: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 20:10:18: #1 total tags in treatment: 5553816 INFO @ Wed, 08 Dec 2021 20:10:18: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:10:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 20:10:18: #1 tags after filtering in treatment: 5131580 INFO @ Wed, 08 Dec 2021 20:10:18: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 20:10:18: #1 finished! INFO @ Wed, 08 Dec 2021 20:10:18: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:10:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:10:18: #2 number of paired peaks: 1561 INFO @ Wed, 08 Dec 2021 20:10:18: start model_add_line... INFO @ Wed, 08 Dec 2021 20:10:18: start X-correlation... INFO @ Wed, 08 Dec 2021 20:10:18: end of X-cor INFO @ Wed, 08 Dec 2021 20:10:18: #2 finished! INFO @ Wed, 08 Dec 2021 20:10:18: #2 predicted fragment length is 244 bps INFO @ Wed, 08 Dec 2021 20:10:18: #2 alternative fragment length(s) may be 244 bps INFO @ Wed, 08 Dec 2021 20:10:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.05_model.r WARNING @ Wed, 08 Dec 2021 20:10:18: #2 Since the d (244) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:10:18: #2 You may need to consider one of the other alternative d(s): 244 WARNING @ Wed, 08 Dec 2021 20:10:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 20:10:18: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:10:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:10:21: 14000000 INFO @ Wed, 08 Dec 2021 20:10:27: 11000000 INFO @ Wed, 08 Dec 2021 20:10:32: 15000000 INFO @ Wed, 08 Dec 2021 20:10:32: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:10:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:10:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:10:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.05_summits.bed INFO @ Wed, 08 Dec 2021 20:10:38: Done! INFO @ Wed, 08 Dec 2021 20:10:39: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 20:10:39: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 20:10:39: #1 total tags in treatment: 5553816 INFO @ Wed, 08 Dec 2021 20:10:39: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:10:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4186 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:10:39: #1 tags after filtering in treatment: 5131580 INFO @ Wed, 08 Dec 2021 20:10:39: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 20:10:39: #1 finished! INFO @ Wed, 08 Dec 2021 20:10:39: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:10:39: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:10:39: #2 number of paired peaks: 1561 INFO @ Wed, 08 Dec 2021 20:10:39: start model_add_line... INFO @ Wed, 08 Dec 2021 20:10:39: start X-correlation... INFO @ Wed, 08 Dec 2021 20:10:39: end of X-cor INFO @ Wed, 08 Dec 2021 20:10:39: #2 finished! INFO @ Wed, 08 Dec 2021 20:10:39: #2 predicted fragment length is 244 bps INFO @ Wed, 08 Dec 2021 20:10:39: #2 alternative fragment length(s) may be 244 bps INFO @ Wed, 08 Dec 2021 20:10:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.10_model.r WARNING @ Wed, 08 Dec 2021 20:10:39: #2 Since the d (244) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:10:39: #2 You may need to consider one of the other alternative d(s): 244 WARNING @ Wed, 08 Dec 2021 20:10:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 20:10:39: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:10:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:10:39: 12000000 INFO @ Wed, 08 Dec 2021 20:10:50: 13000000 INFO @ Wed, 08 Dec 2021 20:10:53: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:10:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:10:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:10:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.10_summits.bed INFO @ Wed, 08 Dec 2021 20:10:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2267 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:11:01: 14000000 INFO @ Wed, 08 Dec 2021 20:11:11: 15000000 INFO @ Wed, 08 Dec 2021 20:11:17: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 20:11:17: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 20:11:17: #1 total tags in treatment: 5553816 INFO @ Wed, 08 Dec 2021 20:11:17: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:11:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 08 Dec 2021 20:11:17: #1 tags after filtering in treatment: 5131580 INFO @ Wed, 08 Dec 2021 20:11:17: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 20:11:17: #1 finished! INFO @ Wed, 08 Dec 2021 20:11:17: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:11:17: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:11:18: #2 number of paired peaks: 1561 INFO @ Wed, 08 Dec 2021 20:11:18: start model_add_line... INFO @ Wed, 08 Dec 2021 20:11:18: start X-correlation... INFO @ Wed, 08 Dec 2021 20:11:18: end of X-cor INFO @ Wed, 08 Dec 2021 20:11:18: #2 finished! INFO @ Wed, 08 Dec 2021 20:11:18: #2 predicted fragment length is 244 bps INFO @ Wed, 08 Dec 2021 20:11:18: #2 alternative fragment length(s) may be 244 bps INFO @ Wed, 08 Dec 2021 20:11:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.20_model.r WARNING @ Wed, 08 Dec 2021 20:11:18: #2 Since the d (244) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 20:11:18: #2 You may need to consider one of the other alternative d(s): 244 WARNING @ Wed, 08 Dec 2021 20:11:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 20:11:18: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:11:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:11:31: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:11:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:11:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:11:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10641188/SRX10641188.20_summits.bed INFO @ Wed, 08 Dec 2021 20:11:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (884 records, 4 fields): 5 millis CompletedMACS2peakCalling