Job ID = 14160319 SRX = SRX9567203 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14331032 spots for SRR13125178/SRR13125178.sra Written 14331032 spots for SRR13125178/SRR13125178.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160475 ("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: 00:25:57 14331032 reads; of these: 14331032 (100.00%) were paired; of these: 5317971 (37.11%) aligned concordantly 0 times 8094217 (56.48%) aligned concordantly exactly 1 time 918844 (6.41%) aligned concordantly >1 times ---- 5317971 pairs aligned concordantly 0 times; of these: 4048672 (76.13%) aligned discordantly 1 time ---- 1269299 pairs aligned 0 times concordantly or discordantly; of these: 2538598 mates make up the pairs; of these: 883677 (34.81%) aligned 0 times 790870 (31.15%) aligned exactly 1 time 864051 (34.04%) aligned >1 times 96.92% overall alignment rate Time searching: 00:25:57 Overall time: 00:25:57 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 24 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] 7251817 / 13056852 = 0.5554 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 01:58:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.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 01:58:26: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:58:26: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:58:35: 1000000 INFO @ Thu, 09 Dec 2021 01:58:43: 2000000 INFO @ Thu, 09 Dec 2021 01:58:51: 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 01:58:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.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 01:58:56: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:58:56: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:59:00: 4000000 INFO @ Thu, 09 Dec 2021 01:59:08: 1000000 INFO @ Thu, 09 Dec 2021 01:59:11: 5000000 INFO @ Thu, 09 Dec 2021 01:59:21: 2000000 INFO @ Thu, 09 Dec 2021 01:59:22: 6000000 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 01:59:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.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 01:59:26: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:59:26: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:59:33: 7000000 INFO @ Thu, 09 Dec 2021 01:59:34: 3000000 INFO @ Thu, 09 Dec 2021 01:59:37: 1000000 INFO @ Thu, 09 Dec 2021 01:59:44: 8000000 INFO @ Thu, 09 Dec 2021 01:59:48: 2000000 INFO @ Thu, 09 Dec 2021 01:59:48: 4000000 INFO @ Thu, 09 Dec 2021 01:59:55: 9000000 INFO @ Thu, 09 Dec 2021 01:59:59: 3000000 INFO @ Thu, 09 Dec 2021 02:00:01: 5000000 INFO @ Thu, 09 Dec 2021 02:00:06: 10000000 INFO @ Thu, 09 Dec 2021 02:00:10: 4000000 INFO @ Thu, 09 Dec 2021 02:00:14: 6000000 INFO @ Thu, 09 Dec 2021 02:00:17: 11000000 INFO @ Thu, 09 Dec 2021 02:00:21: 5000000 INFO @ Thu, 09 Dec 2021 02:00:26: 7000000 INFO @ Thu, 09 Dec 2021 02:00:28: 12000000 INFO @ Thu, 09 Dec 2021 02:00:32: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:00:38: 8000000 INFO @ Thu, 09 Dec 2021 02:00:39: 13000000 INFO @ Thu, 09 Dec 2021 02:00:42: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:00:42: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:00:42: #1 total tags in treatment: 3997724 INFO @ Thu, 09 Dec 2021 02:00:42: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:00:42: #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 02:00:42: #1 tags after filtering in treatment: 3762708 INFO @ Thu, 09 Dec 2021 02:00:42: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 09 Dec 2021 02:00:42: #1 finished! INFO @ Thu, 09 Dec 2021 02:00:42: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:00:42: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:00:42: #2 number of paired peaks: 2081 INFO @ Thu, 09 Dec 2021 02:00:42: start model_add_line... INFO @ Thu, 09 Dec 2021 02:00:42: start X-correlation... INFO @ Thu, 09 Dec 2021 02:00:42: end of X-cor INFO @ Thu, 09 Dec 2021 02:00:42: #2 finished! INFO @ Thu, 09 Dec 2021 02:00:42: #2 predicted fragment length is 287 bps INFO @ Thu, 09 Dec 2021 02:00:42: #2 alternative fragment length(s) may be 287 bps INFO @ Thu, 09 Dec 2021 02:00:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.05_model.r WARNING @ Thu, 09 Dec 2021 02:00:42: #2 Since the d (287) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:00:42: #2 You may need to consider one of the other alternative d(s): 287 WARNING @ Thu, 09 Dec 2021 02:00:42: #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 02:00:42: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:00:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:00:43: 7000000 INFO @ Thu, 09 Dec 2021 02:00:51: 9000000 INFO @ Thu, 09 Dec 2021 02:00:52: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:00:54: 8000000 INFO @ Thu, 09 Dec 2021 02:00:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:00:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:00:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.05_summits.bed INFO @ Thu, 09 Dec 2021 02:00:56: Done! BigWig に変換しました。 pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2474 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:01:03: 10000000 INFO @ Thu, 09 Dec 2021 02:01:04: 9000000 INFO @ Thu, 09 Dec 2021 02:01:15: 10000000 INFO @ Thu, 09 Dec 2021 02:01:16: 11000000 INFO @ Thu, 09 Dec 2021 02:01:26: 11000000 INFO @ Thu, 09 Dec 2021 02:01:29: 12000000 INFO @ Thu, 09 Dec 2021 02:01:37: 12000000 INFO @ Thu, 09 Dec 2021 02:01:42: 13000000 INFO @ Thu, 09 Dec 2021 02:01:45: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:01:45: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:01:45: #1 total tags in treatment: 3997724 INFO @ Thu, 09 Dec 2021 02:01:45: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:01:45: #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 02:01:45: #1 tags after filtering in treatment: 3762708 INFO @ Thu, 09 Dec 2021 02:01:45: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 09 Dec 2021 02:01:45: #1 finished! INFO @ Thu, 09 Dec 2021 02:01:45: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:01:45: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:01:45: #2 number of paired peaks: 2081 INFO @ Thu, 09 Dec 2021 02:01:45: start model_add_line... INFO @ Thu, 09 Dec 2021 02:01:45: start X-correlation... INFO @ Thu, 09 Dec 2021 02:01:46: end of X-cor INFO @ Thu, 09 Dec 2021 02:01:46: #2 finished! INFO @ Thu, 09 Dec 2021 02:01:46: #2 predicted fragment length is 287 bps INFO @ Thu, 09 Dec 2021 02:01:46: #2 alternative fragment length(s) may be 287 bps INFO @ Thu, 09 Dec 2021 02:01:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.10_model.r WARNING @ Thu, 09 Dec 2021 02:01:46: #2 Since the d (287) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:01:46: #2 You may need to consider one of the other alternative d(s): 287 WARNING @ Thu, 09 Dec 2021 02:01:46: #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 02:01:46: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:01:46: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:01:47: 13000000 INFO @ Thu, 09 Dec 2021 02:01:49: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 02:01:49: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 02:01:49: #1 total tags in treatment: 3997724 INFO @ Thu, 09 Dec 2021 02:01:49: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:01:49: #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 02:01:49: #1 tags after filtering in treatment: 3762708 INFO @ Thu, 09 Dec 2021 02:01:49: #1 Redundant rate of treatment: 0.06 INFO @ Thu, 09 Dec 2021 02:01:49: #1 finished! INFO @ Thu, 09 Dec 2021 02:01:49: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:01:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:01:50: #2 number of paired peaks: 2081 INFO @ Thu, 09 Dec 2021 02:01:50: start model_add_line... INFO @ Thu, 09 Dec 2021 02:01:50: start X-correlation... INFO @ Thu, 09 Dec 2021 02:01:50: end of X-cor INFO @ Thu, 09 Dec 2021 02:01:50: #2 finished! INFO @ Thu, 09 Dec 2021 02:01:50: #2 predicted fragment length is 287 bps INFO @ Thu, 09 Dec 2021 02:01:50: #2 alternative fragment length(s) may be 287 bps INFO @ Thu, 09 Dec 2021 02:01:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.20_model.r WARNING @ Thu, 09 Dec 2021 02:01:50: #2 Since the d (287) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 02:01:50: #2 You may need to consider one of the other alternative d(s): 287 WARNING @ Thu, 09 Dec 2021 02:01:50: #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 02:01:50: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:01:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:01:57: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:02:00: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:02:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:02:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:02:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.10_summits.bed INFO @ Thu, 09 Dec 2021 02:02:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (1280 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:02:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:02:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:02:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567203/SRX9567203.20_summits.bed INFO @ Thu, 09 Dec 2021 02:02:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (598 records, 4 fields): 16 millis CompletedMACS2peakCalling