Job ID = 14158418 SRX = SRX10641199 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-08T08:32:20 prefetch.2.10.7: 1) Downloading 'SRR14280079'... 2021-12-08T08:32:20 prefetch.2.10.7: Downloading via HTTPS... 2021-12-08T08:40:01 prefetch.2.10.7: HTTPS download succeed 2021-12-08T08:40:01 prefetch.2.10.7: 1) 'SRR14280079' was downloaded successfully 2021-12-08T08:40:01 prefetch.2.10.7: 'SRR14280079' has 0 unresolved dependencies Read 17100624 spots for SRR14280079/SRR14280079.sra Written 17100624 spots for SRR14280079/SRR14280079.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159210 ("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: 00:27:54 17100624 reads; of these: 17100624 (100.00%) were paired; of these: 10666776 (62.38%) aligned concordantly 0 times 4022883 (23.52%) aligned concordantly exactly 1 time 2410965 (14.10%) aligned concordantly >1 times ---- 10666776 pairs aligned concordantly 0 times; of these: 1529107 (14.34%) aligned discordantly 1 time ---- 9137669 pairs aligned 0 times concordantly or discordantly; of these: 18275338 mates make up the pairs; of these: 17469944 (95.59%) aligned 0 times 416535 (2.28%) aligned exactly 1 time 388859 (2.13%) aligned >1 times 48.92% overall alignment rate Time searching: 00:27:55 Overall time: 00:27:55 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] 1553968 / 7926338 = 0.1961 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 18:18:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.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 18:18:14: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:18:14: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:18:21: 1000000 INFO @ Wed, 08 Dec 2021 18:18:28: 2000000 INFO @ Wed, 08 Dec 2021 18:18:35: 3000000 INFO @ Wed, 08 Dec 2021 18:18:42: 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 @ Wed, 08 Dec 2021 18:18:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.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 18:18:44: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:18:44: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:18:49: 5000000 INFO @ Wed, 08 Dec 2021 18:18:54: 1000000 INFO @ Wed, 08 Dec 2021 18:18:57: 6000000 INFO @ Wed, 08 Dec 2021 18:19:03: 2000000 INFO @ Wed, 08 Dec 2021 18:19:06: 7000000 INFO @ Wed, 08 Dec 2021 18:19:12: 3000000 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 18:19:14: 8000000 INFO @ Wed, 08 Dec 2021 18:19:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.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 18:19:15: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:19:15: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:19:21: 4000000 INFO @ Wed, 08 Dec 2021 18:19:22: 9000000 INFO @ Wed, 08 Dec 2021 18:19:24: 1000000 INFO @ Wed, 08 Dec 2021 18:19:30: 5000000 INFO @ Wed, 08 Dec 2021 18:19:31: 10000000 INFO @ Wed, 08 Dec 2021 18:19:33: 2000000 INFO @ Wed, 08 Dec 2021 18:19:39: 11000000 INFO @ Wed, 08 Dec 2021 18:19:40: 6000000 INFO @ Wed, 08 Dec 2021 18:19:43: 3000000 INFO @ Wed, 08 Dec 2021 18:19:47: 12000000 INFO @ Wed, 08 Dec 2021 18:19:50: 7000000 INFO @ Wed, 08 Dec 2021 18:19:52: 4000000 INFO @ Wed, 08 Dec 2021 18:19:56: 13000000 INFO @ Wed, 08 Dec 2021 18:19:59: 8000000 INFO @ Wed, 08 Dec 2021 18:20:01: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:20:01: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:20:01: #1 total tags in treatment: 5030992 INFO @ Wed, 08 Dec 2021 18:20:01: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:20:01: #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 18:20:01: #1 tags after filtering in treatment: 3870380 INFO @ Wed, 08 Dec 2021 18:20:01: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 18:20:01: #1 finished! INFO @ Wed, 08 Dec 2021 18:20:01: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:20:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:20:01: #2 number of paired peaks: 1337 INFO @ Wed, 08 Dec 2021 18:20:01: start model_add_line... INFO @ Wed, 08 Dec 2021 18:20:01: start X-correlation... INFO @ Wed, 08 Dec 2021 18:20:01: end of X-cor INFO @ Wed, 08 Dec 2021 18:20:01: #2 finished! INFO @ Wed, 08 Dec 2021 18:20:01: #2 predicted fragment length is 253 bps INFO @ Wed, 08 Dec 2021 18:20:01: #2 alternative fragment length(s) may be 253 bps INFO @ Wed, 08 Dec 2021 18:20:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.05_model.r WARNING @ Wed, 08 Dec 2021 18:20:01: #2 Since the d (253) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:20:01: #2 You may need to consider one of the other alternative d(s): 253 WARNING @ Wed, 08 Dec 2021 18:20:01: #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 18:20:01: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:20:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:20:02: 5000000 INFO @ Wed, 08 Dec 2021 18:20:09: 9000000 INFO @ Wed, 08 Dec 2021 18:20:11: 6000000 INFO @ Wed, 08 Dec 2021 18:20:11: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:20:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:20:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:20:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.05_summits.bed INFO @ Wed, 08 Dec 2021 18:20:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2085 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:20:18: 10000000 INFO @ Wed, 08 Dec 2021 18:20:20: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:20:28: 11000000 INFO @ Wed, 08 Dec 2021 18:20:30: 8000000 INFO @ Wed, 08 Dec 2021 18:20:37: 12000000 INFO @ Wed, 08 Dec 2021 18:20:40: 9000000 INFO @ Wed, 08 Dec 2021 18:20:46: 13000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:20:50: 10000000 INFO @ Wed, 08 Dec 2021 18:20:52: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:20:52: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:20:52: #1 total tags in treatment: 5030992 INFO @ Wed, 08 Dec 2021 18:20:52: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:20:52: #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 18:20:52: #1 tags after filtering in treatment: 3870380 INFO @ Wed, 08 Dec 2021 18:20:52: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 18:20:52: #1 finished! INFO @ Wed, 08 Dec 2021 18:20:52: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:20:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:20:52: #2 number of paired peaks: 1337 INFO @ Wed, 08 Dec 2021 18:20:52: start model_add_line... INFO @ Wed, 08 Dec 2021 18:20:52: start X-correlation... INFO @ Wed, 08 Dec 2021 18:20:52: end of X-cor INFO @ Wed, 08 Dec 2021 18:20:52: #2 finished! INFO @ Wed, 08 Dec 2021 18:20:52: #2 predicted fragment length is 253 bps INFO @ Wed, 08 Dec 2021 18:20:52: #2 alternative fragment length(s) may be 253 bps INFO @ Wed, 08 Dec 2021 18:20:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.10_model.r WARNING @ Wed, 08 Dec 2021 18:20:52: #2 Since the d (253) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:20:52: #2 You may need to consider one of the other alternative d(s): 253 WARNING @ Wed, 08 Dec 2021 18:20:52: #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 18:20:52: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:20:52: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:20:59: 11000000 INFO @ Wed, 08 Dec 2021 18:21:03: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:21:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:21:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:21:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.10_summits.bed INFO @ Wed, 08 Dec 2021 18:21:07: Done! INFO @ Wed, 08 Dec 2021 18:21:08: 12000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1145 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:21:17: 13000000 INFO @ Wed, 08 Dec 2021 18:21:22: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:21:22: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:21:22: #1 total tags in treatment: 5030992 INFO @ Wed, 08 Dec 2021 18:21:22: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:21:22: #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 18:21:22: #1 tags after filtering in treatment: 3870380 INFO @ Wed, 08 Dec 2021 18:21:22: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 18:21:22: #1 finished! INFO @ Wed, 08 Dec 2021 18:21:22: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:21:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:21:23: #2 number of paired peaks: 1337 INFO @ Wed, 08 Dec 2021 18:21:23: start model_add_line... INFO @ Wed, 08 Dec 2021 18:21:23: start X-correlation... INFO @ Wed, 08 Dec 2021 18:21:23: end of X-cor INFO @ Wed, 08 Dec 2021 18:21:23: #2 finished! INFO @ Wed, 08 Dec 2021 18:21:23: #2 predicted fragment length is 253 bps INFO @ Wed, 08 Dec 2021 18:21:23: #2 alternative fragment length(s) may be 253 bps INFO @ Wed, 08 Dec 2021 18:21:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.20_model.r WARNING @ Wed, 08 Dec 2021 18:21:23: #2 Since the d (253) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:21:23: #2 You may need to consider one of the other alternative d(s): 253 WARNING @ Wed, 08 Dec 2021 18:21:23: #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 18:21:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:21:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:21:33: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:21:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:21:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:21:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641199/SRX10641199.20_summits.bed INFO @ Wed, 08 Dec 2021 18:21:37: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (565 records, 4 fields): 2 millis CompletedMACS2peakCalling