Job ID = 14158026 SRX = SRX10641218 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 17078397 spots for SRR14280060/SRR14280060.sra Written 17078397 spots for SRR14280060/SRR14280060.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158408 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:37:27 17078397 reads; of these: 17078397 (100.00%) were paired; of these: 9620857 (56.33%) aligned concordantly 0 times 6247162 (36.58%) aligned concordantly exactly 1 time 1210378 (7.09%) aligned concordantly >1 times ---- 9620857 pairs aligned concordantly 0 times; of these: 2825416 (29.37%) aligned discordantly 1 time ---- 6795441 pairs aligned 0 times concordantly or discordantly; of these: 13590882 mates make up the pairs; of these: 12293612 (90.45%) aligned 0 times 660855 (4.86%) aligned exactly 1 time 636415 (4.68%) aligned >1 times 64.01% overall alignment rate Time searching: 00:37:28 Overall time: 00:37:28 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_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] 1254611 / 10253141 = 0.1224 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 14:52:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.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 14:52:06: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:52:06: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:52:23: 1000000 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 14:52:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.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 14:52:35: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:52:35: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:52:40: 2000000 INFO @ Wed, 08 Dec 2021 14:52:51: 1000000 INFO @ Wed, 08 Dec 2021 14:52:56: 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 14:53:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.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 14:53:05: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:53:05: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:53:08: 2000000 INFO @ Wed, 08 Dec 2021 14:53:14: 4000000 INFO @ Wed, 08 Dec 2021 14:53:21: 1000000 INFO @ Wed, 08 Dec 2021 14:53:25: 3000000 INFO @ Wed, 08 Dec 2021 14:53:31: 5000000 INFO @ Wed, 08 Dec 2021 14:53:38: 2000000 INFO @ Wed, 08 Dec 2021 14:53:42: 4000000 INFO @ Wed, 08 Dec 2021 14:53:49: 6000000 INFO @ Wed, 08 Dec 2021 14:53:55: 3000000 INFO @ Wed, 08 Dec 2021 14:54:01: 5000000 INFO @ Wed, 08 Dec 2021 14:54:07: 7000000 INFO @ Wed, 08 Dec 2021 14:54:13: 4000000 INFO @ Wed, 08 Dec 2021 14:54:20: 6000000 INFO @ Wed, 08 Dec 2021 14:54:25: 8000000 INFO @ Wed, 08 Dec 2021 14:54:31: 5000000 INFO @ Wed, 08 Dec 2021 14:54:39: 7000000 INFO @ Wed, 08 Dec 2021 14:54:45: 9000000 INFO @ Wed, 08 Dec 2021 14:54:47: 6000000 INFO @ Wed, 08 Dec 2021 14:54:58: 8000000 INFO @ Wed, 08 Dec 2021 14:55:04: 10000000 INFO @ Wed, 08 Dec 2021 14:55:05: 7000000 INFO @ Wed, 08 Dec 2021 14:55:17: 9000000 INFO @ Wed, 08 Dec 2021 14:55:22: 8000000 INFO @ Wed, 08 Dec 2021 14:55:23: 11000000 INFO @ Wed, 08 Dec 2021 14:55:35: 10000000 INFO @ Wed, 08 Dec 2021 14:55:38: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:55:41: 12000000 INFO @ Wed, 08 Dec 2021 14:55:53: 11000000 INFO @ Wed, 08 Dec 2021 14:55:54: 10000000 INFO @ Wed, 08 Dec 2021 14:56:00: 13000000 INFO @ Wed, 08 Dec 2021 14:56:10: 11000000 INFO @ Wed, 08 Dec 2021 14:56:10: 12000000 INFO @ Wed, 08 Dec 2021 14:56:18: 14000000 INFO @ Wed, 08 Dec 2021 14:56:26: 12000000 INFO @ Wed, 08 Dec 2021 14:56:26: 13000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:56:37: 15000000 INFO @ Wed, 08 Dec 2021 14:56:43: 13000000 INFO @ Wed, 08 Dec 2021 14:56:44: 14000000 INFO @ Wed, 08 Dec 2021 14:56:54: 16000000 INFO @ Wed, 08 Dec 2021 14:56:59: 14000000 INFO @ Wed, 08 Dec 2021 14:57:01: 15000000 INFO @ Wed, 08 Dec 2021 14:57:10: 17000000 INFO @ Wed, 08 Dec 2021 14:57:18: 15000000 INFO @ Wed, 08 Dec 2021 14:57:19: 16000000 INFO @ Wed, 08 Dec 2021 14:57:28: 18000000 INFO @ Wed, 08 Dec 2021 14:57:35: 16000000 INFO @ Wed, 08 Dec 2021 14:57:35: 17000000 INFO @ Wed, 08 Dec 2021 14:57:46: 19000000 INFO @ Wed, 08 Dec 2021 14:57:52: 17000000 INFO @ Wed, 08 Dec 2021 14:57:52: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 14:57:52: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 14:57:52: #1 total tags in treatment: 6467601 INFO @ Wed, 08 Dec 2021 14:57:52: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:57:52: #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 14:57:53: #1 tags after filtering in treatment: 5936995 INFO @ Wed, 08 Dec 2021 14:57:53: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 14:57:53: #1 finished! INFO @ Wed, 08 Dec 2021 14:57:53: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:57:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:57:53: #2 number of paired peaks: 602 WARNING @ Wed, 08 Dec 2021 14:57:53: Fewer paired peaks (602) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 602 pairs to build model! INFO @ Wed, 08 Dec 2021 14:57:53: start model_add_line... INFO @ Wed, 08 Dec 2021 14:57:53: start X-correlation... INFO @ Wed, 08 Dec 2021 14:57:53: end of X-cor INFO @ Wed, 08 Dec 2021 14:57:53: #2 finished! INFO @ Wed, 08 Dec 2021 14:57:53: #2 predicted fragment length is 222 bps INFO @ Wed, 08 Dec 2021 14:57:53: #2 alternative fragment length(s) may be 222 bps INFO @ Wed, 08 Dec 2021 14:57:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.05_model.r WARNING @ Wed, 08 Dec 2021 14:57:53: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:57:53: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Wed, 08 Dec 2021 14:57:53: #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 14:57:53: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:57:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:57:54: 18000000 INFO @ Wed, 08 Dec 2021 14:58:08: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:58:09: 18000000 INFO @ Wed, 08 Dec 2021 14:58:12: 19000000 INFO @ Wed, 08 Dec 2021 14:58:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:58:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:58:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.05_summits.bed INFO @ Wed, 08 Dec 2021 14:58:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (485 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:58:18: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 14:58:18: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 14:58:18: #1 total tags in treatment: 6467601 INFO @ Wed, 08 Dec 2021 14:58:18: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:58:18: #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 14:58:18: #1 tags after filtering in treatment: 5936995 INFO @ Wed, 08 Dec 2021 14:58:18: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 14:58:18: #1 finished! INFO @ Wed, 08 Dec 2021 14:58:18: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:58:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:58:19: #2 number of paired peaks: 602 WARNING @ Wed, 08 Dec 2021 14:58:19: Fewer paired peaks (602) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 602 pairs to build model! INFO @ Wed, 08 Dec 2021 14:58:19: start model_add_line... INFO @ Wed, 08 Dec 2021 14:58:19: start X-correlation... INFO @ Wed, 08 Dec 2021 14:58:19: end of X-cor INFO @ Wed, 08 Dec 2021 14:58:19: #2 finished! INFO @ Wed, 08 Dec 2021 14:58:19: #2 predicted fragment length is 222 bps INFO @ Wed, 08 Dec 2021 14:58:19: #2 alternative fragment length(s) may be 222 bps INFO @ Wed, 08 Dec 2021 14:58:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.10_model.r WARNING @ Wed, 08 Dec 2021 14:58:19: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:58:19: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Wed, 08 Dec 2021 14:58:19: #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 14:58:19: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:58:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:58:26: 19000000 INFO @ Wed, 08 Dec 2021 14:58:32: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 14:58:32: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 14:58:32: #1 total tags in treatment: 6467601 INFO @ Wed, 08 Dec 2021 14:58:32: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:58:32: #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 14:58:32: #1 tags after filtering in treatment: 5936995 INFO @ Wed, 08 Dec 2021 14:58:32: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 14:58:32: #1 finished! INFO @ Wed, 08 Dec 2021 14:58:32: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:58:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:58:32: #2 number of paired peaks: 602 WARNING @ Wed, 08 Dec 2021 14:58:32: Fewer paired peaks (602) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 602 pairs to build model! INFO @ Wed, 08 Dec 2021 14:58:32: start model_add_line... INFO @ Wed, 08 Dec 2021 14:58:32: start X-correlation... INFO @ Wed, 08 Dec 2021 14:58:32: end of X-cor INFO @ Wed, 08 Dec 2021 14:58:32: #2 finished! INFO @ Wed, 08 Dec 2021 14:58:32: #2 predicted fragment length is 222 bps INFO @ Wed, 08 Dec 2021 14:58:32: #2 alternative fragment length(s) may be 222 bps INFO @ Wed, 08 Dec 2021 14:58:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.20_model.r WARNING @ Wed, 08 Dec 2021 14:58:32: #2 Since the d (222) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:58:32: #2 You may need to consider one of the other alternative d(s): 222 WARNING @ Wed, 08 Dec 2021 14:58:32: #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 14:58:32: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:58:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:58:34: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:58:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:58:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:58:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.10_summits.bed INFO @ Wed, 08 Dec 2021 14:58:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (376 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:58:47: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:58:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:58:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:58:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641218/SRX10641218.20_summits.bed INFO @ Wed, 08 Dec 2021 14:58:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (263 records, 4 fields): 2 millis CompletedMACS2peakCalling