Job ID = 8069372 SRX = SRX7217782 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-08-08T03:31:38 prefetch.2.10.7: 1) Downloading 'SRR10533859'... 2020-08-08T03:31:38 prefetch.2.10.7: Downloading via HTTPS... 2020-08-08T03:33:40 prefetch.2.10.7: HTTPS download succeed 2020-08-08T03:33:40 prefetch.2.10.7: 1) 'SRR10533859' was downloaded successfully 2020-08-08T03:33:40 prefetch.2.10.7: 'SRR10533859' has 0 unresolved dependencies Read 8636342 spots for SRR10533859/SRR10533859.sra Written 8636342 spots for SRR10533859/SRR10533859.sra fastq に変換しました。 bowtie でマッピング中... Your job 8070366 ("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: 00:14:59 8636342 reads; of these: 8636342 (100.00%) were paired; of these: 1438457 (16.66%) aligned concordantly 0 times 6491207 (75.16%) aligned concordantly exactly 1 time 706678 (8.18%) aligned concordantly >1 times ---- 1438457 pairs aligned concordantly 0 times; of these: 534905 (37.19%) aligned discordantly 1 time ---- 903552 pairs aligned 0 times concordantly or discordantly; of these: 1807104 mates make up the pairs; of these: 1594522 (88.24%) aligned 0 times 118328 (6.55%) aligned exactly 1 time 94254 (5.22%) aligned >1 times 90.77% overall alignment rate Time searching: 00:14:59 Overall time: 00:14:59 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] 1415809 / 7691129 = 0.1841 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 12:55:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.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 12:55:42: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:55:42: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:55:50: 1000000 INFO @ Sat, 08 Aug 2020 12:55:59: 2000000 INFO @ Sat, 08 Aug 2020 12:56:07: 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 12:56:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.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 12:56:12: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:12: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:17: 4000000 INFO @ Sat, 08 Aug 2020 12:56:22: 1000000 INFO @ Sat, 08 Aug 2020 12:56:27: 5000000 INFO @ Sat, 08 Aug 2020 12:56:33: 2000000 INFO @ Sat, 08 Aug 2020 12:56:38: 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 12:56:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.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 12:56:42: #1 read tag files... INFO @ Sat, 08 Aug 2020 12:56:42: #1 read treatment tags... INFO @ Sat, 08 Aug 2020 12:56:43: 3000000 INFO @ Sat, 08 Aug 2020 12:56:48: 7000000 INFO @ Sat, 08 Aug 2020 12:56:53: 1000000 INFO @ Sat, 08 Aug 2020 12:56:54: 4000000 INFO @ Sat, 08 Aug 2020 12:56:59: 8000000 INFO @ Sat, 08 Aug 2020 12:57:03: 2000000 INFO @ Sat, 08 Aug 2020 12:57:04: 5000000 INFO @ Sat, 08 Aug 2020 12:57:09: 9000000 INFO @ Sat, 08 Aug 2020 12:57:14: 3000000 INFO @ Sat, 08 Aug 2020 12:57:15: 6000000 INFO @ Sat, 08 Aug 2020 12:57:19: 10000000 INFO @ Sat, 08 Aug 2020 12:57:24: 4000000 INFO @ Sat, 08 Aug 2020 12:57:25: 7000000 INFO @ Sat, 08 Aug 2020 12:57:30: 11000000 INFO @ Sat, 08 Aug 2020 12:57:35: 5000000 INFO @ Sat, 08 Aug 2020 12:57:36: 8000000 INFO @ Sat, 08 Aug 2020 12:57:40: 12000000 INFO @ Sat, 08 Aug 2020 12:57:45: 6000000 INFO @ Sat, 08 Aug 2020 12:57:46: 9000000 INFO @ Sat, 08 Aug 2020 12:57:49: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:57:49: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:57:49: #1 total tags in treatment: 5849483 INFO @ Sat, 08 Aug 2020 12:57:49: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:57:49: #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 12:57:49: #1 tags after filtering in treatment: 5225823 INFO @ Sat, 08 Aug 2020 12:57:49: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 12:57:49: #1 finished! INFO @ Sat, 08 Aug 2020 12:57:49: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:57:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:57:49: #2 number of paired peaks: 1685 INFO @ Sat, 08 Aug 2020 12:57:49: start model_add_line... INFO @ Sat, 08 Aug 2020 12:57:49: start X-correlation... INFO @ Sat, 08 Aug 2020 12:57:49: end of X-cor INFO @ Sat, 08 Aug 2020 12:57:49: #2 finished! INFO @ Sat, 08 Aug 2020 12:57:49: #2 predicted fragment length is 209 bps INFO @ Sat, 08 Aug 2020 12:57:49: #2 alternative fragment length(s) may be 209 bps INFO @ Sat, 08 Aug 2020 12:57:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.05_model.r WARNING @ Sat, 08 Aug 2020 12:57:49: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:57:49: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Sat, 08 Aug 2020 12:57:49: #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 12:57:49: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:57:49: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 08 Aug 2020 12:57:55: 7000000 INFO @ Sat, 08 Aug 2020 12:57:56: 10000000 INFO @ Sat, 08 Aug 2020 12:58:03: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:58:04: 8000000 INFO @ Sat, 08 Aug 2020 12:58:05: 11000000 INFO @ Sat, 08 Aug 2020 12:58:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.05_peaks.xls INFO @ Sat, 08 Aug 2020 12:58:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.05_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:58:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.05_summits.bed INFO @ Sat, 08 Aug 2020 12:58:10: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6223 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:58:13: 9000000 INFO @ Sat, 08 Aug 2020 12:58:14: 12000000 BigWig に変換しました。 INFO @ Sat, 08 Aug 2020 12:58:21: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:21: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:21: #1 total tags in treatment: 5849483 INFO @ Sat, 08 Aug 2020 12:58:21: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:21: #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 12:58:22: #1 tags after filtering in treatment: 5225823 INFO @ Sat, 08 Aug 2020 12:58:22: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 12:58:22: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:22: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:22: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:22: 10000000 INFO @ Sat, 08 Aug 2020 12:58:22: #2 number of paired peaks: 1685 INFO @ Sat, 08 Aug 2020 12:58:22: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:22: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:22: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:22: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:22: #2 predicted fragment length is 209 bps INFO @ Sat, 08 Aug 2020 12:58:22: #2 alternative fragment length(s) may be 209 bps INFO @ Sat, 08 Aug 2020 12:58:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.10_model.r WARNING @ Sat, 08 Aug 2020 12:58:22: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:58:22: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Sat, 08 Aug 2020 12:58:22: #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 12:58:22: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:58:30: 11000000 INFO @ Sat, 08 Aug 2020 12:58:35: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:58:38: 12000000 INFO @ Sat, 08 Aug 2020 12:58:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.10_peaks.xls INFO @ Sat, 08 Aug 2020 12:58:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.10_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:58:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.10_summits.bed INFO @ Sat, 08 Aug 2020 12:58:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3763 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 08 Aug 2020 12:58:45: #1 tag size is determined as 150 bps INFO @ Sat, 08 Aug 2020 12:58:45: #1 tag size = 150 INFO @ Sat, 08 Aug 2020 12:58:45: #1 total tags in treatment: 5849483 INFO @ Sat, 08 Aug 2020 12:58:45: #1 user defined the maximum tags... INFO @ Sat, 08 Aug 2020 12:58:45: #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 12:58:45: #1 tags after filtering in treatment: 5225823 INFO @ Sat, 08 Aug 2020 12:58:45: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 08 Aug 2020 12:58:45: #1 finished! INFO @ Sat, 08 Aug 2020 12:58:45: #2 Build Peak Model... INFO @ Sat, 08 Aug 2020 12:58:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Aug 2020 12:58:46: #2 number of paired peaks: 1685 INFO @ Sat, 08 Aug 2020 12:58:46: start model_add_line... INFO @ Sat, 08 Aug 2020 12:58:46: start X-correlation... INFO @ Sat, 08 Aug 2020 12:58:46: end of X-cor INFO @ Sat, 08 Aug 2020 12:58:46: #2 finished! INFO @ Sat, 08 Aug 2020 12:58:46: #2 predicted fragment length is 209 bps INFO @ Sat, 08 Aug 2020 12:58:46: #2 alternative fragment length(s) may be 209 bps INFO @ Sat, 08 Aug 2020 12:58:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.20_model.r WARNING @ Sat, 08 Aug 2020 12:58:46: #2 Since the d (209) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Aug 2020 12:58:46: #2 You may need to consider one of the other alternative d(s): 209 WARNING @ Sat, 08 Aug 2020 12:58:46: #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 12:58:46: #3 Call peaks... INFO @ Sat, 08 Aug 2020 12:58:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Aug 2020 12:58:58: #3 Call peaks for each chromosome... INFO @ Sat, 08 Aug 2020 12:59:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.20_peaks.xls INFO @ Sat, 08 Aug 2020 12:59:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.20_peaks.narrowPeak INFO @ Sat, 08 Aug 2020 12:59:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7217782/SRX7217782.20_summits.bed INFO @ Sat, 08 Aug 2020 12:59:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1768 records, 4 fields): 3 millis CompletedMACS2peakCalling