Job ID = 12264830 SRX = SRX7687153 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 27001433 spots for SRR11034896/SRR11034896.sra Written 27001433 spots for SRR11034896/SRR11034896.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265410 ("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: 00:33:30 27001433 reads; of these: 27001433 (100.00%) were paired; of these: 5906246 (21.87%) aligned concordantly 0 times 18587759 (68.84%) aligned concordantly exactly 1 time 2507428 (9.29%) aligned concordantly >1 times ---- 5906246 pairs aligned concordantly 0 times; of these: 2866322 (48.53%) aligned discordantly 1 time ---- 3039924 pairs aligned 0 times concordantly or discordantly; of these: 6079848 mates make up the pairs; of these: 5175080 (85.12%) aligned 0 times 401552 (6.60%) aligned exactly 1 time 503216 (8.28%) aligned >1 times 90.42% overall alignment rate Time searching: 00:33:30 Overall time: 00:33:30 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] 14170312 / 23915577 = 0.5925 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 06:43:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.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 06:43:25: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:43:25: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:43:33: 1000000 INFO @ Sat, 03 Apr 2021 06:43:40: 2000000 INFO @ Sat, 03 Apr 2021 06:43:48: 3000000 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 06:43:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.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 06:43:55: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:43:55: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:43:56: 4000000 INFO @ Sat, 03 Apr 2021 06:44:05: 1000000 INFO @ Sat, 03 Apr 2021 06:44:05: 5000000 INFO @ Sat, 03 Apr 2021 06:44:17: 2000000 INFO @ Sat, 03 Apr 2021 06:44:17: 6000000 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 06:44:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.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 06:44:25: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:44:25: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:44:28: 3000000 INFO @ Sat, 03 Apr 2021 06:44:29: 7000000 INFO @ Sat, 03 Apr 2021 06:44:39: 4000000 INFO @ Sat, 03 Apr 2021 06:44:39: 1000000 INFO @ Sat, 03 Apr 2021 06:44:40: 8000000 INFO @ Sat, 03 Apr 2021 06:44:49: 5000000 INFO @ Sat, 03 Apr 2021 06:44:50: 9000000 INFO @ Sat, 03 Apr 2021 06:44:52: 2000000 INFO @ Sat, 03 Apr 2021 06:44:58: 6000000 INFO @ Sat, 03 Apr 2021 06:44:59: 10000000 INFO @ Sat, 03 Apr 2021 06:45:05: 3000000 INFO @ Sat, 03 Apr 2021 06:45:08: 7000000 INFO @ Sat, 03 Apr 2021 06:45:09: 11000000 INFO @ Sat, 03 Apr 2021 06:45:18: 8000000 INFO @ Sat, 03 Apr 2021 06:45:18: 4000000 INFO @ Sat, 03 Apr 2021 06:45:18: 12000000 INFO @ Sat, 03 Apr 2021 06:45:27: 9000000 INFO @ Sat, 03 Apr 2021 06:45:28: 13000000 INFO @ Sat, 03 Apr 2021 06:45:30: 5000000 INFO @ Sat, 03 Apr 2021 06:45:37: 10000000 INFO @ Sat, 03 Apr 2021 06:45:37: 14000000 INFO @ Sat, 03 Apr 2021 06:45:42: 6000000 INFO @ Sat, 03 Apr 2021 06:45:46: 11000000 INFO @ Sat, 03 Apr 2021 06:45:47: 15000000 INFO @ Sat, 03 Apr 2021 06:45:54: 7000000 INFO @ Sat, 03 Apr 2021 06:45:56: 12000000 INFO @ Sat, 03 Apr 2021 06:45:56: 16000000 INFO @ Sat, 03 Apr 2021 06:46:06: 17000000 INFO @ Sat, 03 Apr 2021 06:46:06: 8000000 INFO @ Sat, 03 Apr 2021 06:46:06: 13000000 INFO @ Sat, 03 Apr 2021 06:46:15: 18000000 INFO @ Sat, 03 Apr 2021 06:46:16: 14000000 INFO @ Sat, 03 Apr 2021 06:46:18: 9000000 INFO @ Sat, 03 Apr 2021 06:46:24: 19000000 INFO @ Sat, 03 Apr 2021 06:46:25: 15000000 INFO @ Sat, 03 Apr 2021 06:46:29: 10000000 INFO @ Sat, 03 Apr 2021 06:46:32: 20000000 INFO @ Sat, 03 Apr 2021 06:46:35: 16000000 INFO @ Sat, 03 Apr 2021 06:46:36: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:46:36: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:46:36: #1 total tags in treatment: 8514196 INFO @ Sat, 03 Apr 2021 06:46:36: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:46:36: #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 06:46:37: #1 tags after filtering in treatment: 6547193 INFO @ Sat, 03 Apr 2021 06:46:37: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 06:46:37: #1 finished! INFO @ Sat, 03 Apr 2021 06:46:37: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:46:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:46:37: #2 number of paired peaks: 433 WARNING @ Sat, 03 Apr 2021 06:46:37: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Sat, 03 Apr 2021 06:46:37: start model_add_line... INFO @ Sat, 03 Apr 2021 06:46:37: start X-correlation... INFO @ Sat, 03 Apr 2021 06:46:37: end of X-cor INFO @ Sat, 03 Apr 2021 06:46:37: #2 finished! INFO @ Sat, 03 Apr 2021 06:46:37: #2 predicted fragment length is 128 bps INFO @ Sat, 03 Apr 2021 06:46:37: #2 alternative fragment length(s) may be 4,128,147,163 bps INFO @ Sat, 03 Apr 2021 06:46:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.05_model.r WARNING @ Sat, 03 Apr 2021 06:46:37: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:46:37: #2 You may need to consider one of the other alternative d(s): 4,128,147,163 WARNING @ Sat, 03 Apr 2021 06:46:37: #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 06:46:37: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:46:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:46:41: 11000000 INFO @ Sat, 03 Apr 2021 06:46:44: 17000000 INFO @ Sat, 03 Apr 2021 06:46:53: 12000000 INFO @ Sat, 03 Apr 2021 06:46:54: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:46:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:47:03: 19000000 INFO @ Sat, 03 Apr 2021 06:47:05: 13000000 INFO @ Sat, 03 Apr 2021 06:47:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:47:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:47:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.05_summits.bed INFO @ Sat, 03 Apr 2021 06:47:10: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (984 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:47:12: 20000000 INFO @ Sat, 03 Apr 2021 06:47:16: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:47:16: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:47:16: #1 total tags in treatment: 8514196 INFO @ Sat, 03 Apr 2021 06:47:16: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:47:16: #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 06:47:16: #1 tags after filtering in treatment: 6547193 INFO @ Sat, 03 Apr 2021 06:47:16: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 06:47:16: #1 finished! INFO @ Sat, 03 Apr 2021 06:47:16: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:47:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:47:16: 14000000 INFO @ Sat, 03 Apr 2021 06:47:16: #2 number of paired peaks: 433 WARNING @ Sat, 03 Apr 2021 06:47:16: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Sat, 03 Apr 2021 06:47:16: start model_add_line... INFO @ Sat, 03 Apr 2021 06:47:16: start X-correlation... INFO @ Sat, 03 Apr 2021 06:47:16: end of X-cor INFO @ Sat, 03 Apr 2021 06:47:16: #2 finished! INFO @ Sat, 03 Apr 2021 06:47:16: #2 predicted fragment length is 128 bps INFO @ Sat, 03 Apr 2021 06:47:16: #2 alternative fragment length(s) may be 4,128,147,163 bps INFO @ Sat, 03 Apr 2021 06:47:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.10_model.r WARNING @ Sat, 03 Apr 2021 06:47:16: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:47:16: #2 You may need to consider one of the other alternative d(s): 4,128,147,163 WARNING @ Sat, 03 Apr 2021 06:47:16: #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 06:47:16: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:47:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:47:27: 15000000 INFO @ Sat, 03 Apr 2021 06:47:36: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:47:38: 16000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:47:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:47:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:47:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.10_summits.bed INFO @ Sat, 03 Apr 2021 06:47:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (456 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:47:50: 17000000 INFO @ Sat, 03 Apr 2021 06:48:00: 18000000 INFO @ Sat, 03 Apr 2021 06:48:11: 19000000 INFO @ Sat, 03 Apr 2021 06:48:21: 20000000 INFO @ Sat, 03 Apr 2021 06:48:26: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 06:48:26: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 06:48:26: #1 total tags in treatment: 8514196 INFO @ Sat, 03 Apr 2021 06:48:26: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:48:26: #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 06:48:26: #1 tags after filtering in treatment: 6547193 INFO @ Sat, 03 Apr 2021 06:48:26: #1 Redundant rate of treatment: 0.23 INFO @ Sat, 03 Apr 2021 06:48:26: #1 finished! INFO @ Sat, 03 Apr 2021 06:48:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:48:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:48:27: #2 number of paired peaks: 433 WARNING @ Sat, 03 Apr 2021 06:48:27: Fewer paired peaks (433) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 433 pairs to build model! INFO @ Sat, 03 Apr 2021 06:48:27: start model_add_line... INFO @ Sat, 03 Apr 2021 06:48:27: start X-correlation... INFO @ Sat, 03 Apr 2021 06:48:27: end of X-cor INFO @ Sat, 03 Apr 2021 06:48:27: #2 finished! INFO @ Sat, 03 Apr 2021 06:48:27: #2 predicted fragment length is 128 bps INFO @ Sat, 03 Apr 2021 06:48:27: #2 alternative fragment length(s) may be 4,128,147,163 bps INFO @ Sat, 03 Apr 2021 06:48:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.20_model.r WARNING @ Sat, 03 Apr 2021 06:48:27: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:48:27: #2 You may need to consider one of the other alternative d(s): 4,128,147,163 WARNING @ Sat, 03 Apr 2021 06:48:27: #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 06:48:27: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:48:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:48:47: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:48:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:48:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:48:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7687153/SRX7687153.20_summits.bed INFO @ Sat, 03 Apr 2021 06:48:59: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (186 records, 4 fields): 2 millis CompletedMACS2peakCalling