Job ID = 14160353 SRX = SRX9567177 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 18839971 spots for SRR13125152/SRR13125152.sra Written 18839971 spots for SRR13125152/SRR13125152.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160570 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:48:20 18839971 reads; of these: 18839971 (100.00%) were paired; of these: 8798066 (46.70%) aligned concordantly 0 times 6794987 (36.07%) aligned concordantly exactly 1 time 3246918 (17.23%) aligned concordantly >1 times ---- 8798066 pairs aligned concordantly 0 times; of these: 6034876 (68.59%) aligned discordantly 1 time ---- 2763190 pairs aligned 0 times concordantly or discordantly; of these: 5526380 mates make up the pairs; of these: 2460580 (44.52%) aligned 0 times 1453138 (26.29%) aligned exactly 1 time 1612662 (29.18%) aligned >1 times 93.47% overall alignment rate Time searching: 00:48:20 Overall time: 00:48:20 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 28 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] 10692018 / 16063044 = 0.6656 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 02:42:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.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 02:42:55: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:42:55: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:43:03: 1000000 INFO @ Thu, 09 Dec 2021 02:43:11: 2000000 INFO @ Thu, 09 Dec 2021 02:43:19: 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 @ Thu, 09 Dec 2021 02:43:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.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 02:43:25: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:43:25: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:43:27: 4000000 INFO @ Thu, 09 Dec 2021 02:43:37: 1000000 INFO @ Thu, 09 Dec 2021 02:43:38: 5000000 INFO @ Thu, 09 Dec 2021 02:43:48: 6000000 INFO @ Thu, 09 Dec 2021 02:43:49: 2000000 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 02:43:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.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 02:43:55: #1 read tag files... INFO @ Thu, 09 Dec 2021 02:43:55: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 02:43:59: 7000000 INFO @ Thu, 09 Dec 2021 02:44:02: 3000000 INFO @ Thu, 09 Dec 2021 02:44:06: 1000000 INFO @ Thu, 09 Dec 2021 02:44:10: 8000000 INFO @ Thu, 09 Dec 2021 02:44:14: 4000000 INFO @ Thu, 09 Dec 2021 02:44:18: 2000000 INFO @ Thu, 09 Dec 2021 02:44:20: 9000000 INFO @ Thu, 09 Dec 2021 02:44:27: 5000000 INFO @ Thu, 09 Dec 2021 02:44:30: 3000000 INFO @ Thu, 09 Dec 2021 02:44:31: 10000000 INFO @ Thu, 09 Dec 2021 02:44:40: 6000000 INFO @ Thu, 09 Dec 2021 02:44:42: 4000000 INFO @ Thu, 09 Dec 2021 02:44:42: 11000000 INFO @ Thu, 09 Dec 2021 02:44:52: 7000000 INFO @ Thu, 09 Dec 2021 02:44:53: 12000000 INFO @ Thu, 09 Dec 2021 02:44:54: 5000000 INFO @ Thu, 09 Dec 2021 02:45:04: 13000000 INFO @ Thu, 09 Dec 2021 02:45:05: 8000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:45:06: 6000000 INFO @ Thu, 09 Dec 2021 02:45:13: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:45:13: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:45:13: #1 total tags in treatment: 3459535 INFO @ Thu, 09 Dec 2021 02:45:13: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:45:13: #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 02:45:13: #1 tags after filtering in treatment: 2658735 INFO @ Thu, 09 Dec 2021 02:45:13: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 09 Dec 2021 02:45:13: #1 finished! INFO @ Thu, 09 Dec 2021 02:45:13: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:45:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:45:13: #2 number of paired peaks: 1123 INFO @ Thu, 09 Dec 2021 02:45:13: start model_add_line... INFO @ Thu, 09 Dec 2021 02:45:13: start X-correlation... INFO @ Thu, 09 Dec 2021 02:45:13: end of X-cor INFO @ Thu, 09 Dec 2021 02:45:13: #2 finished! INFO @ Thu, 09 Dec 2021 02:45:13: #2 predicted fragment length is 286 bps INFO @ Thu, 09 Dec 2021 02:45:13: #2 alternative fragment length(s) may be 286 bps INFO @ Thu, 09 Dec 2021 02:45:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.05_model.r WARNING @ Thu, 09 Dec 2021 02:45:13: #2 Since the d (286) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:45:13: #2 You may need to consider one of the other alternative d(s): 286 WARNING @ Thu, 09 Dec 2021 02:45:13: #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 02:45:13: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:45:13: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:45:17: 9000000 INFO @ Thu, 09 Dec 2021 02:45:18: 7000000 INFO @ Thu, 09 Dec 2021 02:45:21: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:45:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:45:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:45:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.05_summits.bed INFO @ Thu, 09 Dec 2021 02:45:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (769 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:45:30: 10000000 INFO @ Thu, 09 Dec 2021 02:45:30: 8000000 INFO @ Thu, 09 Dec 2021 02:45:42: 9000000 INFO @ Thu, 09 Dec 2021 02:45:42: 11000000 INFO @ Thu, 09 Dec 2021 02:45:54: 10000000 INFO @ Thu, 09 Dec 2021 02:45:55: 12000000 INFO @ Thu, 09 Dec 2021 02:46:06: 11000000 INFO @ Thu, 09 Dec 2021 02:46:07: 13000000 INFO @ Thu, 09 Dec 2021 02:46:17: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:46:17: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:46:17: #1 total tags in treatment: 3459535 INFO @ Thu, 09 Dec 2021 02:46:17: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:46:17: #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 02:46:17: #1 tags after filtering in treatment: 2658735 INFO @ Thu, 09 Dec 2021 02:46:17: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 09 Dec 2021 02:46:17: #1 finished! INFO @ Thu, 09 Dec 2021 02:46:17: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:46:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:46:18: #2 number of paired peaks: 1123 INFO @ Thu, 09 Dec 2021 02:46:18: start model_add_line... INFO @ Thu, 09 Dec 2021 02:46:18: start X-correlation... INFO @ Thu, 09 Dec 2021 02:46:18: end of X-cor INFO @ Thu, 09 Dec 2021 02:46:18: #2 finished! INFO @ Thu, 09 Dec 2021 02:46:18: #2 predicted fragment length is 286 bps INFO @ Thu, 09 Dec 2021 02:46:18: #2 alternative fragment length(s) may be 286 bps INFO @ Thu, 09 Dec 2021 02:46:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.10_model.r WARNING @ Thu, 09 Dec 2021 02:46:18: #2 Since the d (286) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:46:18: #2 You may need to consider one of the other alternative d(s): 286 WARNING @ Thu, 09 Dec 2021 02:46:18: #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 02:46:18: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:46:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:46:18: 12000000 INFO @ Thu, 09 Dec 2021 02:46:25: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:46:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:46:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:46:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.10_summits.bed INFO @ Thu, 09 Dec 2021 02:46:28: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (594 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:46:29: 13000000 INFO @ Thu, 09 Dec 2021 02:46:38: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:46:38: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:46:38: #1 total tags in treatment: 3459535 INFO @ Thu, 09 Dec 2021 02:46:38: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:46:38: #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 02:46:38: #1 tags after filtering in treatment: 2658735 INFO @ Thu, 09 Dec 2021 02:46:38: #1 Redundant rate of treatment: 0.23 INFO @ Thu, 09 Dec 2021 02:46:38: #1 finished! INFO @ Thu, 09 Dec 2021 02:46:38: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:46:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:46:38: #2 number of paired peaks: 1123 INFO @ Thu, 09 Dec 2021 02:46:38: start model_add_line... INFO @ Thu, 09 Dec 2021 02:46:38: start X-correlation... INFO @ Thu, 09 Dec 2021 02:46:38: end of X-cor INFO @ Thu, 09 Dec 2021 02:46:38: #2 finished! INFO @ Thu, 09 Dec 2021 02:46:38: #2 predicted fragment length is 286 bps INFO @ Thu, 09 Dec 2021 02:46:38: #2 alternative fragment length(s) may be 286 bps INFO @ Thu, 09 Dec 2021 02:46:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.20_model.r WARNING @ Thu, 09 Dec 2021 02:46:38: #2 Since the d (286) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:46:38: #2 You may need to consider one of the other alternative d(s): 286 WARNING @ Thu, 09 Dec 2021 02:46:38: #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 02:46:38: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:46:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:46:46: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:46:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:46:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:46:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567177/SRX9567177.20_summits.bed INFO @ Thu, 09 Dec 2021 02:46:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (439 records, 4 fields): 2 millis CompletedMACS2peakCalling