Job ID = 14158415 SRX = SRX10641198 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20443983 spots for SRR14280080/SRR14280080.sra Written 20443983 spots for SRR14280080/SRR14280080.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159169 ("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: 00:24:47 20443983 reads; of these: 20443983 (100.00%) were paired; of these: 15451598 (75.58%) aligned concordantly 0 times 3119480 (15.26%) aligned concordantly exactly 1 time 1872905 (9.16%) aligned concordantly >1 times ---- 15451598 pairs aligned concordantly 0 times; of these: 1726777 (11.18%) aligned discordantly 1 time ---- 13724821 pairs aligned 0 times concordantly or discordantly; of these: 27449642 mates make up the pairs; of these: 26441917 (96.33%) aligned 0 times 515152 (1.88%) aligned exactly 1 time 492573 (1.79%) aligned >1 times 35.33% overall alignment rate Time searching: 00:24:47 Overall time: 00:24:47 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] 1495758 / 6691051 = 0.2235 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 18:05:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.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 18:05:22: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:05:22: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:05:28: 1000000 INFO @ Wed, 08 Dec 2021 18:05:34: 2000000 INFO @ Wed, 08 Dec 2021 18:05:40: 3000000 INFO @ Wed, 08 Dec 2021 18:05:47: 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 18:05:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.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 18:05:52: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:05:52: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:05:53: 5000000 INFO @ Wed, 08 Dec 2021 18:05:58: 1000000 INFO @ Wed, 08 Dec 2021 18:05:59: 6000000 INFO @ Wed, 08 Dec 2021 18:06:04: 2000000 INFO @ Wed, 08 Dec 2021 18:06:06: 7000000 INFO @ Wed, 08 Dec 2021 18:06:11: 3000000 INFO @ Wed, 08 Dec 2021 18:06:12: 8000000 INFO @ Wed, 08 Dec 2021 18:06:17: 4000000 INFO @ Wed, 08 Dec 2021 18:06:19: 9000000 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 18:06:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.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 18:06:22: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:06:22: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:06:24: 5000000 INFO @ Wed, 08 Dec 2021 18:06:25: 10000000 INFO @ Wed, 08 Dec 2021 18:06:28: 1000000 INFO @ Wed, 08 Dec 2021 18:06:30: 6000000 INFO @ Wed, 08 Dec 2021 18:06:31: 11000000 INFO @ Wed, 08 Dec 2021 18:06:34: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:06:34: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:06:34: #1 total tags in treatment: 3749149 INFO @ Wed, 08 Dec 2021 18:06:34: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:06:34: #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 18:06:34: #1 tags after filtering in treatment: 2898528 INFO @ Wed, 08 Dec 2021 18:06:34: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 18:06:34: #1 finished! INFO @ Wed, 08 Dec 2021 18:06:34: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:06:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:06:35: 2000000 INFO @ Wed, 08 Dec 2021 18:06:35: #2 number of paired peaks: 1021 INFO @ Wed, 08 Dec 2021 18:06:35: start model_add_line... INFO @ Wed, 08 Dec 2021 18:06:35: start X-correlation... INFO @ Wed, 08 Dec 2021 18:06:35: end of X-cor INFO @ Wed, 08 Dec 2021 18:06:35: #2 finished! INFO @ Wed, 08 Dec 2021 18:06:35: #2 predicted fragment length is 258 bps INFO @ Wed, 08 Dec 2021 18:06:35: #2 alternative fragment length(s) may be 258 bps INFO @ Wed, 08 Dec 2021 18:06:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.05_model.r WARNING @ Wed, 08 Dec 2021 18:06:35: #2 Since the d (258) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:06:35: #2 You may need to consider one of the other alternative d(s): 258 WARNING @ Wed, 08 Dec 2021 18:06:35: #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 18:06:35: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:06:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:06:37: 7000000 INFO @ Wed, 08 Dec 2021 18:06:41: 3000000 INFO @ Wed, 08 Dec 2021 18:06:43: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:06:43: 8000000 INFO @ Wed, 08 Dec 2021 18:06:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:06:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:06:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.05_summits.bed INFO @ Wed, 08 Dec 2021 18:06:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (871 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:06:48: 4000000 INFO @ Wed, 08 Dec 2021 18:06:50: 9000000 INFO @ Wed, 08 Dec 2021 18:06:54: 5000000 INFO @ Wed, 08 Dec 2021 18:06:56: 10000000 INFO @ Wed, 08 Dec 2021 18:07:00: 6000000 INFO @ Wed, 08 Dec 2021 18:07:02: 11000000 INFO @ Wed, 08 Dec 2021 18:07:05: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:07:05: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:07:05: #1 total tags in treatment: 3749149 INFO @ Wed, 08 Dec 2021 18:07:05: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:07:05: #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 18:07:05: #1 tags after filtering in treatment: 2898528 INFO @ Wed, 08 Dec 2021 18:07:05: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 18:07:05: #1 finished! INFO @ Wed, 08 Dec 2021 18:07:05: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:07:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:07:06: #2 number of paired peaks: 1021 INFO @ Wed, 08 Dec 2021 18:07:06: start model_add_line... INFO @ Wed, 08 Dec 2021 18:07:06: start X-correlation... INFO @ Wed, 08 Dec 2021 18:07:06: end of X-cor INFO @ Wed, 08 Dec 2021 18:07:06: #2 finished! INFO @ Wed, 08 Dec 2021 18:07:06: #2 predicted fragment length is 258 bps INFO @ Wed, 08 Dec 2021 18:07:06: #2 alternative fragment length(s) may be 258 bps INFO @ Wed, 08 Dec 2021 18:07:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.10_model.r WARNING @ Wed, 08 Dec 2021 18:07:06: #2 Since the d (258) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:07:06: #2 You may need to consider one of the other alternative d(s): 258 WARNING @ Wed, 08 Dec 2021 18:07:06: #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 18:07:06: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:07:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:07:07: 7000000 INFO @ Wed, 08 Dec 2021 18:07:13: 8000000 INFO @ Wed, 08 Dec 2021 18:07:13: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:07:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:07:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:07:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.10_summits.bed INFO @ Wed, 08 Dec 2021 18:07:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (605 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:07:19: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:07:26: 10000000 INFO @ Wed, 08 Dec 2021 18:07:32: 11000000 INFO @ Wed, 08 Dec 2021 18:07:35: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:07:35: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:07:35: #1 total tags in treatment: 3749149 INFO @ Wed, 08 Dec 2021 18:07:35: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:07:35: #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 18:07:35: #1 tags after filtering in treatment: 2898528 INFO @ Wed, 08 Dec 2021 18:07:35: #1 Redundant rate of treatment: 0.23 INFO @ Wed, 08 Dec 2021 18:07:35: #1 finished! INFO @ Wed, 08 Dec 2021 18:07:35: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:07:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:07:35: #2 number of paired peaks: 1021 INFO @ Wed, 08 Dec 2021 18:07:35: start model_add_line... INFO @ Wed, 08 Dec 2021 18:07:35: start X-correlation... INFO @ Wed, 08 Dec 2021 18:07:35: end of X-cor INFO @ Wed, 08 Dec 2021 18:07:35: #2 finished! INFO @ Wed, 08 Dec 2021 18:07:35: #2 predicted fragment length is 258 bps INFO @ Wed, 08 Dec 2021 18:07:35: #2 alternative fragment length(s) may be 258 bps INFO @ Wed, 08 Dec 2021 18:07:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.20_model.r WARNING @ Wed, 08 Dec 2021 18:07:35: #2 Since the d (258) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:07:35: #2 You may need to consider one of the other alternative d(s): 258 WARNING @ Wed, 08 Dec 2021 18:07:35: #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 18:07:35: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:07:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:07:43: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:07:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:07:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:07:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641198/SRX10641198.20_summits.bed INFO @ Wed, 08 Dec 2021 18:07:46: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (397 records, 4 fields): 3 millis CompletedMACS2peakCalling