Job ID = 8069425 SRX = SRX8392418 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:32:30 prefetch.2.10.7: 1) Downloading 'SRR11842071'... 2020-08-08T03:32:30 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:34:29 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:34:29 prefetch.2.10.7: 1) 'SRR11842071' was downloaded successfully 2020-08-08T03:34:29 prefetch.2.10.7: 'SRR11842071' has 0 unresolved dependencies Read 8304521 spots for SRR11842071/SRR11842071.sra Written 8304521 spots for SRR11842071/SRR11842071.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070403 ("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: 00:14:51 8304521 reads; of these: 8304521 (100.00%) were paired; of these: 696868 (8.39%) aligned concordantly 0 times 6826916 (82.21%) aligned concordantly exactly 1 time 780737 (9.40%) aligned concordantly >1 times ---- 696868 pairs aligned concordantly 0 times; of these: 302606 (43.42%) aligned discordantly 1 time ---- 394262 pairs aligned 0 times concordantly or discordantly; of these: 788524 mates make up the pairs; of these: 594172 (75.35%) aligned 0 times 119826 (15.20%) aligned exactly 1 time 74526 (9.45%) aligned >1 times 96.42% overall alignment rate Time searching: 00:14:51 Overall time: 00:14:51 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 12 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] 1973859 / 7867728 = 0.2509 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 12:56:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.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 @ Sat, 08 Aug 2020 12:56:33: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:33: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:42: 1000000 INFO @ Sat, 08 Aug 2020 12:56:50: 2000000 INFO @ Sat, 08 Aug 2020 12:56:59: 3000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 12:57:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.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 @ Sat, 08 Aug 2020 12:57:03: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:57:03: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:57:09: 4000000 INFO @ Sat, 08 Aug 2020 12:57:14: 1000000 INFO @ Sat, 08 Aug 2020 12:57:19: 5000000 INFO @ Sat, 08 Aug 2020 12:57:25: 2000000 INFO @ Sat, 08 Aug 2020 12:57:28: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 08 Aug 2020 12:57:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.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 @ Sat, 08 Aug 2020 12:57:33: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:57:33: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:57:36: 3000000 INFO @ Sat, 08 Aug 2020 12:57:38: 7000000 INFO @ Sat, 08 Aug 2020 12:57:44: 1000000 INFO @ Sat, 08 Aug 2020 12:57:47: 4000000 INFO @ Sat, 08 Aug 2020 12:57:47: 8000000 INFO @ Sat, 08 Aug 2020 12:57:54: 2000000 INFO @ Sat, 08 Aug 2020 12:57:57: 9000000 INFO @ Sat, 08 Aug 2020 12:57:58: 5000000 INFO @ Sat, 08 Aug 2020 12:58:04: 3000000 INFO @ Sat, 08 Aug 2020 12:58:07: 10000000 INFO @ Sat, 08 Aug 2020 12:58:09: 6000000 INFO @ Sat, 08 Aug 2020 12:58:15: 4000000 INFO @ Sat, 08 Aug 2020 12:58:16: 11000000 INFO @ Sat, 08 Aug 2020 12:58:20: 7000000 INFO @ Sat, 08 Aug 2020 12:58:25: 5000000 INFO @ Sat, 08 Aug 2020 12:58:26: 12000000 INFO @ Sat, 08 Aug 2020 12:58:26: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:26: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:26: #1 total tags in treatment: 5669578 INFO @ Sat, 08 Aug 2020 12:58:26: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:58:26: #1 tags after filtering in treatment: 5246511 INFO @ Sat, 08 Aug 2020 12:58:26: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 12:58:26: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:26: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:27: #2 number of paired peaks: 1117 INFO @ Sat, 08 Aug 2020 12:58:27: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:27: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:27: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:27: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:27: #2 predicted fragment length is 226 bps INFO @ Sat, 08 Aug 2020 12:58:27: #2 alternative fragment length(s) may be 226 bps INFO @ Sat, 08 Aug 2020 12:58:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.05_model.r WARNING @ Sat, 08 Aug 2020 12:58:27: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:58:27: #2 You may need to consider one of the other alternative d(s): 226 WARNING @ Sat, 08 Aug 2020 12:58:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:58:27: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:58:31: 8000000 INFO @ Sat, 08 Aug 2020 12:58:35: 6000000 INFO @ Sat, 08 Aug 2020 12:58:39: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:58:42: 9000000 INFO @ Sat, 08 Aug 2020 12:58:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:58:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:58:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.05_summits.bed INFO @ Sat, 08 Aug 2020 12:58:44: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (6398 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:58:45: 7000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:58:53: 10000000 INFO @ Sat, 08 Aug 2020 12:58:55: 8000000 INFO @ Sat, 08 Aug 2020 12:59:04: 11000000 INFO @ Sat, 08 Aug 2020 12:59:05: 9000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:59:14: 12000000 INFO @ Sat, 08 Aug 2020 12:59:15: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:59:15: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:59:15: #1 total tags in treatment: 5669578 INFO @ Sat, 08 Aug 2020 12:59:15: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:59:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Aug 2020 12:59:15: #1 tags after filtering in treatment: 5246511 INFO @ Sat, 08 Aug 2020 12:59:15: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 12:59:15: #1 finished! INFO @ Sat, 08 Aug 2020 12:59:15: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:59:15: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:59:15: #2 number of paired peaks: 1117 INFO @ Sat, 08 Aug 2020 12:59:15: start model_add_line... INFO @ Sat, 08 Aug 2020 12:59:15: 10000000 INFO @ Sat, 08 Aug 2020 12:59:15: start X-correlation... INFO @ Sat, 08 Aug 2020 12:59:15: end of X-cor INFO @ Sat, 08 Aug 2020 12:59:15: #2 finished! INFO @ Sat, 08 Aug 2020 12:59:15: #2 predicted fragment length is 226 bps INFO @ Sat, 08 Aug 2020 12:59:15: #2 alternative fragment length(s) may be 226 bps INFO @ Sat, 08 Aug 2020 12:59:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.10_model.r WARNING @ Sat, 08 Aug 2020 12:59:15: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:59:15: #2 You may need to consider one of the other alternative d(s): 226 WARNING @ Sat, 08 Aug 2020 12:59:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:59:15: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:59:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:59:24: 11000000 INFO @ Sat, 08 Aug 2020 12:59:28: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:59:34: 12000000 INFO @ Sat, 08 Aug 2020 12:59:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:59:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:59:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.10_summits.bed INFO @ Sat, 08 Aug 2020 12:59:34: Done! INFO @ Sat, 08 Aug 2020 12:59:34: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:59:34: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:59:34: #1 total tags in treatment: 5669578 INFO @ Sat, 08 Aug 2020 12:59:34: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:59:34: #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 INFO @ Sat, 08 Aug 2020 12:59:34: #1 tags after filtering in treatment: 5246511 INFO @ Sat, 08 Aug 2020 12:59:34: #1 Redundant rate of treatment: 0.07 INFO @ Sat, 08 Aug 2020 12:59:34: #1 finished! INFO @ Sat, 08 Aug 2020 12:59:34: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:59:34: #2 looking for paired plus/minus strand peaks... pass2 - checking and writing primary data (3607 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:59:35: #2 number of paired peaks: 1117 INFO @ Sat, 08 Aug 2020 12:59:35: start model_add_line... INFO @ Sat, 08 Aug 2020 12:59:35: start X-correlation... INFO @ Sat, 08 Aug 2020 12:59:35: end of X-cor INFO @ Sat, 08 Aug 2020 12:59:35: #2 finished! INFO @ Sat, 08 Aug 2020 12:59:35: #2 predicted fragment length is 226 bps INFO @ Sat, 08 Aug 2020 12:59:35: #2 alternative fragment length(s) may be 226 bps INFO @ Sat, 08 Aug 2020 12:59:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.20_model.r WARNING @ Sat, 08 Aug 2020 12:59:35: #2 Since the d (226) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:59:35: #2 You may need to consider one of the other alternative d(s): 226 WARNING @ Sat, 08 Aug 2020 12:59:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Aug 2020 12:59:35: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:59:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:59:47: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:59:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:59:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:59:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8392418/SRX8392418.20_summits.bed INFO @ Sat, 08 Aug 2020 12:59:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1384 records, 4 fields): 2 millis CompletedMACS2peakCalling