Job ID = 12264746 SRX = SRX2332999 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 29523880 spots for SRR5000679/SRR5000679.sra Written 29523880 spots for SRR5000679/SRR5000679.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265162 ("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: 00:09:28 29523880 reads; of these: 29523880 (100.00%) were paired; of these: 27669502 (93.72%) aligned concordantly 0 times 1346430 (4.56%) aligned concordantly exactly 1 time 507948 (1.72%) aligned concordantly >1 times ---- 27669502 pairs aligned concordantly 0 times; of these: 307965 (1.11%) aligned discordantly 1 time ---- 27361537 pairs aligned 0 times concordantly or discordantly; of these: 54723074 mates make up the pairs; of these: 54466517 (99.53%) aligned 0 times 67119 (0.12%) aligned exactly 1 time 189438 (0.35%) aligned >1 times 7.76% overall alignment rate Time searching: 00:09:28 Overall time: 00:09:28 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_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] 553483 / 2149472 = 0.2575 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:07:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.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, 03 Apr 2021 06:07:16: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:07:16: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:07:23: 1000000 INFO @ Sat, 03 Apr 2021 06:07:29: 2000000 INFO @ Sat, 03 Apr 2021 06:07:36: 3000000 INFO @ Sat, 03 Apr 2021 06:07:39: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:07:39: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:07:39: #1 total tags in treatment: 1357138 INFO @ Sat, 03 Apr 2021 06:07:39: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:07:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:07:39: #1 tags after filtering in treatment: 1071385 INFO @ Sat, 03 Apr 2021 06:07:39: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 06:07:39: #1 finished! INFO @ Sat, 03 Apr 2021 06:07:39: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:07:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:07:39: #2 number of paired peaks: 1088 INFO @ Sat, 03 Apr 2021 06:07:39: start model_add_line... INFO @ Sat, 03 Apr 2021 06:07:39: start X-correlation... INFO @ Sat, 03 Apr 2021 06:07:39: end of X-cor INFO @ Sat, 03 Apr 2021 06:07:39: #2 finished! INFO @ Sat, 03 Apr 2021 06:07:39: #2 predicted fragment length is 166 bps INFO @ Sat, 03 Apr 2021 06:07:39: #2 alternative fragment length(s) may be 166 bps INFO @ Sat, 03 Apr 2021 06:07:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.05_model.r WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:07:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.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, 03 Apr 2021 06:07:42: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:07:42: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:07:48: 1000000 WARNING @ Sat, 03 Apr 2021 06:07:55: #2 Since the d (166) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:07:55: #2 You may need to consider one of the other alternative d(s): 166 WARNING @ Sat, 03 Apr 2021 06:07:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:07:55: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:07:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:07:55: 2000000 INFO @ Sat, 03 Apr 2021 06:07:57: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:07:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:07:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:07:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.05_summits.bed INFO @ Sat, 03 Apr 2021 06:07:59: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (867 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:08:01: 3000000 INFO @ Sat, 03 Apr 2021 06:08:04: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:08:04: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:08:04: #1 total tags in treatment: 1357138 INFO @ Sat, 03 Apr 2021 06:08:04: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:08:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:08:04: #1 tags after filtering in treatment: 1071385 INFO @ Sat, 03 Apr 2021 06:08:04: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 06:08:04: #1 finished! INFO @ Sat, 03 Apr 2021 06:08:04: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:08:04: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:08:04: #2 number of paired peaks: 1088 INFO @ Sat, 03 Apr 2021 06:08:04: start model_add_line... INFO @ Sat, 03 Apr 2021 06:08:05: start X-correlation... INFO @ Sat, 03 Apr 2021 06:08:05: end of X-cor INFO @ Sat, 03 Apr 2021 06:08:05: #2 finished! INFO @ Sat, 03 Apr 2021 06:08:05: #2 predicted fragment length is 166 bps INFO @ Sat, 03 Apr 2021 06:08:05: #2 alternative fragment length(s) may be 166 bps INFO @ Sat, 03 Apr 2021 06:08:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.10_model.r WARNING @ Sat, 03 Apr 2021 06:08:05: #2 Since the d (166) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:08:05: #2 You may need to consider one of the other alternative d(s): 166 WARNING @ Sat, 03 Apr 2021 06:08:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:08:05: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:08:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:08:07: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:08:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:08:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:08:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.10_summits.bed INFO @ Sat, 03 Apr 2021 06:08:08: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (368 records, 4 fields): 77 millis CompletedMACS2peakCalling BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:08:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.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, 03 Apr 2021 06:08:12: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:08:12: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:08:18: 1000000 INFO @ Sat, 03 Apr 2021 06:08:24: 2000000 INFO @ Sat, 03 Apr 2021 06:08:31: 3000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:08:34: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:08:34: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:08:34: #1 total tags in treatment: 1357138 INFO @ Sat, 03 Apr 2021 06:08:34: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:08:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:08:34: #1 tags after filtering in treatment: 1071385 INFO @ Sat, 03 Apr 2021 06:08:34: #1 Redundant rate of treatment: 0.21 INFO @ Sat, 03 Apr 2021 06:08:34: #1 finished! INFO @ Sat, 03 Apr 2021 06:08:34: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:08:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:08:34: #2 number of paired peaks: 1088 INFO @ Sat, 03 Apr 2021 06:08:34: start model_add_line... INFO @ Sat, 03 Apr 2021 06:08:34: start X-correlation... INFO @ Sat, 03 Apr 2021 06:08:34: end of X-cor INFO @ Sat, 03 Apr 2021 06:08:34: #2 finished! INFO @ Sat, 03 Apr 2021 06:08:34: #2 predicted fragment length is 166 bps INFO @ Sat, 03 Apr 2021 06:08:34: #2 alternative fragment length(s) may be 166 bps INFO @ Sat, 03 Apr 2021 06:08:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.20_model.r WARNING @ Sat, 03 Apr 2021 06:08:34: #2 Since the d (166) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:08:34: #2 You may need to consider one of the other alternative d(s): 166 WARNING @ Sat, 03 Apr 2021 06:08:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:08:34: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:08:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:08:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:08:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:08:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:08:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2332999/SRX2332999.20_summits.bed INFO @ Sat, 03 Apr 2021 06:08:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (128 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。