Job ID = 14158414 SRX = SRX10641197 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15821510 spots for SRR14280081/SRR14280081.sra Written 15821510 spots for SRR14280081/SRR14280081.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159170 ("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: 00:26:32 15821510 reads; of these: 15821510 (100.00%) were paired; of these: 6460373 (40.83%) aligned concordantly 0 times 7934288 (50.15%) aligned concordantly exactly 1 time 1426849 (9.02%) aligned concordantly >1 times ---- 6460373 pairs aligned concordantly 0 times; of these: 2077180 (32.15%) aligned discordantly 1 time ---- 4383193 pairs aligned 0 times concordantly or discordantly; of these: 8766386 mates make up the pairs; of these: 7891721 (90.02%) aligned 0 times 434415 (4.96%) aligned exactly 1 time 440250 (5.02%) aligned >1 times 75.06% overall alignment rate Time searching: 00:26:32 Overall time: 00:26:32 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 20 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] 1391807 / 11394720 = 0.1221 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 18:11:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.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 18:11:50: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:11:50: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:12:00: 1000000 INFO @ Wed, 08 Dec 2021 18:12:09: 2000000 INFO @ Wed, 08 Dec 2021 18:12:18: 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 18:12:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.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 18:12:20: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:12:20: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:12:26: 4000000 INFO @ Wed, 08 Dec 2021 18:12:31: 1000000 INFO @ Wed, 08 Dec 2021 18:12:35: 5000000 INFO @ Wed, 08 Dec 2021 18:12:42: 2000000 INFO @ Wed, 08 Dec 2021 18:12:44: 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 @ Wed, 08 Dec 2021 18:12:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.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 18:12:50: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:12:50: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:12:52: 3000000 INFO @ Wed, 08 Dec 2021 18:12:53: 7000000 INFO @ Wed, 08 Dec 2021 18:13:01: 1000000 INFO @ Wed, 08 Dec 2021 18:13:01: 4000000 INFO @ Wed, 08 Dec 2021 18:13:02: 8000000 INFO @ Wed, 08 Dec 2021 18:13:11: 5000000 INFO @ Wed, 08 Dec 2021 18:13:11: 9000000 INFO @ Wed, 08 Dec 2021 18:13:12: 2000000 INFO @ Wed, 08 Dec 2021 18:13:20: 6000000 INFO @ Wed, 08 Dec 2021 18:13:20: 10000000 INFO @ Wed, 08 Dec 2021 18:13:23: 3000000 INFO @ Wed, 08 Dec 2021 18:13:29: 7000000 INFO @ Wed, 08 Dec 2021 18:13:29: 11000000 INFO @ Wed, 08 Dec 2021 18:13:32: 4000000 INFO @ Wed, 08 Dec 2021 18:13:38: 8000000 INFO @ Wed, 08 Dec 2021 18:13:38: 12000000 INFO @ Wed, 08 Dec 2021 18:13:41: 5000000 INFO @ Wed, 08 Dec 2021 18:13:47: 9000000 INFO @ Wed, 08 Dec 2021 18:13:47: 13000000 INFO @ Wed, 08 Dec 2021 18:13:50: 6000000 INFO @ Wed, 08 Dec 2021 18:13:56: 10000000 INFO @ Wed, 08 Dec 2021 18:13:56: 14000000 INFO @ Wed, 08 Dec 2021 18:13:59: 7000000 INFO @ Wed, 08 Dec 2021 18:14:05: 11000000 INFO @ Wed, 08 Dec 2021 18:14:05: 15000000 INFO @ Wed, 08 Dec 2021 18:14:09: 8000000 INFO @ Wed, 08 Dec 2021 18:14:14: 12000000 INFO @ Wed, 08 Dec 2021 18:14:15: 16000000 INFO @ Wed, 08 Dec 2021 18:14:18: 9000000 INFO @ Wed, 08 Dec 2021 18:14:23: 13000000 INFO @ Wed, 08 Dec 2021 18:14:24: 17000000 INFO @ Wed, 08 Dec 2021 18:14:27: 10000000 INFO @ Wed, 08 Dec 2021 18:14:33: 14000000 INFO @ Wed, 08 Dec 2021 18:14:33: 18000000 INFO @ Wed, 08 Dec 2021 18:14:36: 11000000 INFO @ Wed, 08 Dec 2021 18:14:42: 15000000 INFO @ Wed, 08 Dec 2021 18:14:42: 19000000 INFO @ Wed, 08 Dec 2021 18:14:45: 12000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:14:51: 16000000 INFO @ Wed, 08 Dec 2021 18:14:51: 20000000 INFO @ Wed, 08 Dec 2021 18:14:54: 13000000 INFO @ Wed, 08 Dec 2021 18:15:00: 17000000 INFO @ Wed, 08 Dec 2021 18:15:00: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:15:00: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:15:00: #1 total tags in treatment: 8164910 INFO @ Wed, 08 Dec 2021 18:15:00: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:15:00: #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 18:15:00: #1 tags after filtering in treatment: 7620801 INFO @ Wed, 08 Dec 2021 18:15:00: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:15:00: #1 finished! INFO @ Wed, 08 Dec 2021 18:15:00: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:15:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:15:01: #2 number of paired peaks: 486 WARNING @ Wed, 08 Dec 2021 18:15:01: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Wed, 08 Dec 2021 18:15:01: start model_add_line... INFO @ Wed, 08 Dec 2021 18:15:01: start X-correlation... INFO @ Wed, 08 Dec 2021 18:15:01: end of X-cor INFO @ Wed, 08 Dec 2021 18:15:01: #2 finished! INFO @ Wed, 08 Dec 2021 18:15:01: #2 predicted fragment length is 219 bps INFO @ Wed, 08 Dec 2021 18:15:01: #2 alternative fragment length(s) may be 219 bps INFO @ Wed, 08 Dec 2021 18:15:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.05_model.r WARNING @ Wed, 08 Dec 2021 18:15:01: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:15:01: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Wed, 08 Dec 2021 18:15:01: #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 18:15:01: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:15:01: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:15:03: 14000000 INFO @ Wed, 08 Dec 2021 18:15:09: 18000000 INFO @ Wed, 08 Dec 2021 18:15:12: 15000000 INFO @ Wed, 08 Dec 2021 18:15:17: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:15:18: 19000000 INFO @ Wed, 08 Dec 2021 18:15:21: 16000000 INFO @ Wed, 08 Dec 2021 18:15:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:15:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:15:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.05_summits.bed INFO @ Wed, 08 Dec 2021 18:15:24: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (442 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:15:27: 20000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:15:30: 17000000 INFO @ Wed, 08 Dec 2021 18:15:36: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:15:36: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:15:36: #1 total tags in treatment: 8164910 INFO @ Wed, 08 Dec 2021 18:15:36: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:15:36: #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 18:15:36: #1 tags after filtering in treatment: 7620801 INFO @ Wed, 08 Dec 2021 18:15:36: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:15:36: #1 finished! INFO @ Wed, 08 Dec 2021 18:15:36: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:15:36: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:15:36: #2 number of paired peaks: 486 WARNING @ Wed, 08 Dec 2021 18:15:36: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Wed, 08 Dec 2021 18:15:36: start model_add_line... INFO @ Wed, 08 Dec 2021 18:15:36: start X-correlation... INFO @ Wed, 08 Dec 2021 18:15:36: end of X-cor INFO @ Wed, 08 Dec 2021 18:15:36: #2 finished! INFO @ Wed, 08 Dec 2021 18:15:36: #2 predicted fragment length is 219 bps INFO @ Wed, 08 Dec 2021 18:15:36: #2 alternative fragment length(s) may be 219 bps INFO @ Wed, 08 Dec 2021 18:15:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.10_model.r WARNING @ Wed, 08 Dec 2021 18:15:36: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:15:36: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Wed, 08 Dec 2021 18:15:36: #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 18:15:36: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:15:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:15:39: 18000000 INFO @ Wed, 08 Dec 2021 18:15:47: 19000000 INFO @ Wed, 08 Dec 2021 18:15:53: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:15:55: 20000000 INFO @ Wed, 08 Dec 2021 18:16:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:16:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:16:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.10_summits.bed INFO @ Wed, 08 Dec 2021 18:16:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (347 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:16:03: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 18:16:03: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 18:16:03: #1 total tags in treatment: 8164910 INFO @ Wed, 08 Dec 2021 18:16:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:16:03: #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 18:16:04: #1 tags after filtering in treatment: 7620801 INFO @ Wed, 08 Dec 2021 18:16:04: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:16:04: #1 finished! INFO @ Wed, 08 Dec 2021 18:16:04: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:16:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:16:04: #2 number of paired peaks: 486 WARNING @ Wed, 08 Dec 2021 18:16:04: Fewer paired peaks (486) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 486 pairs to build model! INFO @ Wed, 08 Dec 2021 18:16:04: start model_add_line... INFO @ Wed, 08 Dec 2021 18:16:04: start X-correlation... INFO @ Wed, 08 Dec 2021 18:16:04: end of X-cor INFO @ Wed, 08 Dec 2021 18:16:04: #2 finished! INFO @ Wed, 08 Dec 2021 18:16:04: #2 predicted fragment length is 219 bps INFO @ Wed, 08 Dec 2021 18:16:04: #2 alternative fragment length(s) may be 219 bps INFO @ Wed, 08 Dec 2021 18:16:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.20_model.r WARNING @ Wed, 08 Dec 2021 18:16:04: #2 Since the d (219) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 18:16:04: #2 You may need to consider one of the other alternative d(s): 219 WARNING @ Wed, 08 Dec 2021 18:16:04: #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 18:16:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:16:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:16:20: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:16:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:16:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:16:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641197/SRX10641197.20_summits.bed INFO @ Wed, 08 Dec 2021 18:16:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (257 records, 4 fields): 1 millis CompletedMACS2peakCalling