Job ID = 14157956 SRX = SRX10641212 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 19461580 spots for SRR14280066/SRR14280066.sra Written 19461580 spots for SRR14280066/SRR14280066.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158237 ("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: 00:24:01 19461580 reads; of these: 19461580 (100.00%) were paired; of these: 12159321 (62.48%) aligned concordantly 0 times 6269708 (32.22%) aligned concordantly exactly 1 time 1032551 (5.31%) aligned concordantly >1 times ---- 12159321 pairs aligned concordantly 0 times; of these: 2658501 (21.86%) aligned discordantly 1 time ---- 9500820 pairs aligned 0 times concordantly or discordantly; of these: 19001640 mates make up the pairs; of these: 17771301 (93.53%) aligned 0 times 682471 (3.59%) aligned exactly 1 time 547868 (2.88%) aligned >1 times 54.34% overall alignment rate Time searching: 00:24:02 Overall time: 00:24:02 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 16 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] 1464938 / 9924340 = 0.1476 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 13:54:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.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 13:54:51: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:54:51: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:54:58: 1000000 INFO @ Wed, 08 Dec 2021 13:55:05: 2000000 INFO @ Wed, 08 Dec 2021 13:55:12: 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 @ Wed, 08 Dec 2021 13:55:19: 4000000 INFO @ Wed, 08 Dec 2021 13:55:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.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 13:55:20: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:55:20: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:55:27: 5000000 INFO @ Wed, 08 Dec 2021 13:55:29: 1000000 INFO @ Wed, 08 Dec 2021 13:55:35: 6000000 INFO @ Wed, 08 Dec 2021 13:55:38: 2000000 INFO @ Wed, 08 Dec 2021 13:55:43: 7000000 INFO @ Wed, 08 Dec 2021 13:55:48: 3000000 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 13:55:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.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 13:55:50: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:55:50: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:55:51: 8000000 INFO @ Wed, 08 Dec 2021 13:55:58: 4000000 INFO @ Wed, 08 Dec 2021 13:56:00: 9000000 INFO @ Wed, 08 Dec 2021 13:56:00: 1000000 INFO @ Wed, 08 Dec 2021 13:56:07: 5000000 INFO @ Wed, 08 Dec 2021 13:56:08: 10000000 INFO @ Wed, 08 Dec 2021 13:56:09: 2000000 INFO @ Wed, 08 Dec 2021 13:56:16: 11000000 INFO @ Wed, 08 Dec 2021 13:56:17: 6000000 INFO @ Wed, 08 Dec 2021 13:56:18: 3000000 INFO @ Wed, 08 Dec 2021 13:56:24: 12000000 INFO @ Wed, 08 Dec 2021 13:56:27: 7000000 INFO @ Wed, 08 Dec 2021 13:56:28: 4000000 INFO @ Wed, 08 Dec 2021 13:56:33: 13000000 INFO @ Wed, 08 Dec 2021 13:56:37: 8000000 INFO @ Wed, 08 Dec 2021 13:56:37: 5000000 INFO @ Wed, 08 Dec 2021 13:56:41: 14000000 INFO @ Wed, 08 Dec 2021 13:56:46: 9000000 INFO @ Wed, 08 Dec 2021 13:56:46: 6000000 INFO @ Wed, 08 Dec 2021 13:56:49: 15000000 INFO @ Wed, 08 Dec 2021 13:56:55: 10000000 INFO @ Wed, 08 Dec 2021 13:56:56: 7000000 INFO @ Wed, 08 Dec 2021 13:56:57: 16000000 INFO @ Wed, 08 Dec 2021 13:57:04: 11000000 INFO @ Wed, 08 Dec 2021 13:57:05: 17000000 INFO @ Wed, 08 Dec 2021 13:57:06: 8000000 INFO @ Wed, 08 Dec 2021 13:57:13: 12000000 INFO @ Wed, 08 Dec 2021 13:57:14: 18000000 INFO @ Wed, 08 Dec 2021 13:57:15: 9000000 INFO @ Wed, 08 Dec 2021 13:57:16: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:57:16: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:57:16: #1 total tags in treatment: 6152240 INFO @ Wed, 08 Dec 2021 13:57:16: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:57:16: #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 13:57:16: #1 tags after filtering in treatment: 5705301 INFO @ Wed, 08 Dec 2021 13:57:16: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 13:57:16: #1 finished! INFO @ Wed, 08 Dec 2021 13:57:16: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:57:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:57:16: #2 number of paired peaks: 530 WARNING @ Wed, 08 Dec 2021 13:57:16: Fewer paired peaks (530) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 530 pairs to build model! INFO @ Wed, 08 Dec 2021 13:57:16: start model_add_line... INFO @ Wed, 08 Dec 2021 13:57:16: start X-correlation... INFO @ Wed, 08 Dec 2021 13:57:16: end of X-cor INFO @ Wed, 08 Dec 2021 13:57:16: #2 finished! INFO @ Wed, 08 Dec 2021 13:57:16: #2 predicted fragment length is 223 bps INFO @ Wed, 08 Dec 2021 13:57:16: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 08 Dec 2021 13:57:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.05_model.r WARNING @ Wed, 08 Dec 2021 13:57:16: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:57:16: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 08 Dec 2021 13:57:16: #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 13:57:16: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:57:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:57:23: 13000000 INFO @ Wed, 08 Dec 2021 13:57:24: 10000000 INFO @ Wed, 08 Dec 2021 13:57:30: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 13:57:32: 14000000 INFO @ Wed, 08 Dec 2021 13:57:33: 11000000 INFO @ Wed, 08 Dec 2021 13:57:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.05_peaks.xls INFO @ Wed, 08 Dec 2021 13:57:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:57:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.05_summits.bed INFO @ Wed, 08 Dec 2021 13:57:36: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (436 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:57:41: 15000000 INFO @ Wed, 08 Dec 2021 13:57:42: 12000000 INFO @ Wed, 08 Dec 2021 13:57:50: 16000000 INFO @ Wed, 08 Dec 2021 13:57:51: 13000000 INFO @ Wed, 08 Dec 2021 13:57:59: 17000000 INFO @ Wed, 08 Dec 2021 13:58:01: 14000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 13:58:09: 18000000 INFO @ Wed, 08 Dec 2021 13:58:10: 15000000 INFO @ Wed, 08 Dec 2021 13:58:11: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:58:11: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:58:11: #1 total tags in treatment: 6152240 INFO @ Wed, 08 Dec 2021 13:58:11: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:58:11: #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 13:58:11: #1 tags after filtering in treatment: 5705301 INFO @ Wed, 08 Dec 2021 13:58:11: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 13:58:11: #1 finished! INFO @ Wed, 08 Dec 2021 13:58:11: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:58:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:58:12: #2 number of paired peaks: 530 WARNING @ Wed, 08 Dec 2021 13:58:12: Fewer paired peaks (530) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 530 pairs to build model! INFO @ Wed, 08 Dec 2021 13:58:12: start model_add_line... INFO @ Wed, 08 Dec 2021 13:58:12: start X-correlation... INFO @ Wed, 08 Dec 2021 13:58:12: end of X-cor INFO @ Wed, 08 Dec 2021 13:58:12: #2 finished! INFO @ Wed, 08 Dec 2021 13:58:12: #2 predicted fragment length is 223 bps INFO @ Wed, 08 Dec 2021 13:58:12: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 08 Dec 2021 13:58:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.10_model.r WARNING @ Wed, 08 Dec 2021 13:58:12: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:58:12: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 08 Dec 2021 13:58:12: #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 13:58:12: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:58:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:58:18: 16000000 INFO @ Wed, 08 Dec 2021 13:58:26: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:58:27: 17000000 INFO @ Wed, 08 Dec 2021 13:58:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.10_peaks.xls INFO @ Wed, 08 Dec 2021 13:58:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:58:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.10_summits.bed INFO @ Wed, 08 Dec 2021 13:58:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (318 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:58:36: 18000000 INFO @ Wed, 08 Dec 2021 13:58:38: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:58:38: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:58:38: #1 total tags in treatment: 6152240 INFO @ Wed, 08 Dec 2021 13:58:38: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:58:38: #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 13:58:38: #1 tags after filtering in treatment: 5705301 INFO @ Wed, 08 Dec 2021 13:58:38: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 13:58:38: #1 finished! INFO @ Wed, 08 Dec 2021 13:58:38: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:58:38: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:58:38: #2 number of paired peaks: 530 WARNING @ Wed, 08 Dec 2021 13:58:38: Fewer paired peaks (530) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 530 pairs to build model! INFO @ Wed, 08 Dec 2021 13:58:38: start model_add_line... INFO @ Wed, 08 Dec 2021 13:58:39: start X-correlation... INFO @ Wed, 08 Dec 2021 13:58:39: end of X-cor INFO @ Wed, 08 Dec 2021 13:58:39: #2 finished! INFO @ Wed, 08 Dec 2021 13:58:39: #2 predicted fragment length is 223 bps INFO @ Wed, 08 Dec 2021 13:58:39: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 08 Dec 2021 13:58:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.20_model.r WARNING @ Wed, 08 Dec 2021 13:58:39: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 13:58:39: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 08 Dec 2021 13:58:39: #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 13:58:39: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:58:39: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:58:52: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:58:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.20_peaks.xls INFO @ Wed, 08 Dec 2021 13:58:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:58:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641212/SRX10641212.20_summits.bed INFO @ Wed, 08 Dec 2021 13:58:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (229 records, 4 fields): 2 millis CompletedMACS2peakCalling