Job ID = 14157955 SRX = SRX10641211 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2021-12-08T04:16:28 prefetch.2.10.7: 1) Downloading 'SRR14280067'... 2021-12-08T04:16:28 prefetch.2.10.7: Downloading via HTTPS... 2021-12-08T04:18:26 prefetch.2.10.7: HTTPS download succeed 2021-12-08T04:18:26 prefetch.2.10.7: 1) 'SRR14280067' was downloaded successfully 2021-12-08T04:18:26 prefetch.2.10.7: 'SRR14280067' has 0 unresolved dependencies Read 15829063 spots for SRR14280067/SRR14280067.sra Written 15829063 spots for SRR14280067/SRR14280067.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158232 ("srTce11") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:17:59 15829063 reads; of these: 15829063 (100.00%) were paired; of these: 11555567 (73.00%) aligned concordantly 0 times 3551151 (22.43%) aligned concordantly exactly 1 time 722345 (4.56%) aligned concordantly >1 times ---- 11555567 pairs aligned concordantly 0 times; of these: 2458298 (21.27%) aligned discordantly 1 time ---- 9097269 pairs aligned 0 times concordantly or discordantly; of these: 18194538 mates make up the pairs; of these: 16897203 (92.87%) aligned 0 times 756283 (4.16%) aligned exactly 1 time 541052 (2.97%) aligned >1 times 46.63% overall alignment rate Time searching: 00:18:00 Overall time: 00:18:00 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 12 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] 864535 / 6711290 = 0.1288 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 13:46:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.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 13:46:02: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:46:02: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:46:10: 1000000 INFO @ Wed, 08 Dec 2021 13:46:18: 2000000 INFO @ Wed, 08 Dec 2021 13:46:26: 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 13:46:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.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 13:46:31: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:46:31: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:46:35: 4000000 INFO @ Wed, 08 Dec 2021 13:46:40: 1000000 INFO @ Wed, 08 Dec 2021 13:46:44: 5000000 INFO @ Wed, 08 Dec 2021 13:46:49: 2000000 INFO @ Wed, 08 Dec 2021 13:46:53: 6000000 INFO @ Wed, 08 Dec 2021 13:46:58: 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 13:47:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.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 13:47:01: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:47:01: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:47:02: 7000000 INFO @ Wed, 08 Dec 2021 13:47:07: 4000000 INFO @ Wed, 08 Dec 2021 13:47:10: 1000000 INFO @ Wed, 08 Dec 2021 13:47:11: 8000000 INFO @ Wed, 08 Dec 2021 13:47:16: 5000000 INFO @ Wed, 08 Dec 2021 13:47:20: 2000000 INFO @ Wed, 08 Dec 2021 13:47:21: 9000000 INFO @ Wed, 08 Dec 2021 13:47:26: 6000000 INFO @ Wed, 08 Dec 2021 13:47:28: 3000000 INFO @ Wed, 08 Dec 2021 13:47:29: 10000000 INFO @ Wed, 08 Dec 2021 13:47:35: 7000000 INFO @ Wed, 08 Dec 2021 13:47:37: 11000000 INFO @ Wed, 08 Dec 2021 13:47:37: 4000000 INFO @ Wed, 08 Dec 2021 13:47:44: 8000000 INFO @ Wed, 08 Dec 2021 13:47:45: 5000000 INFO @ Wed, 08 Dec 2021 13:47:45: 12000000 INFO @ Wed, 08 Dec 2021 13:47:53: 6000000 INFO @ Wed, 08 Dec 2021 13:47:53: 9000000 INFO @ Wed, 08 Dec 2021 13:47:55: 13000000 INFO @ Wed, 08 Dec 2021 13:47:55: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:47:55: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:47:55: #1 total tags in treatment: 3664643 INFO @ Wed, 08 Dec 2021 13:47:55: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:47:55: #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 13:47:55: #1 tags after filtering in treatment: 3393026 INFO @ Wed, 08 Dec 2021 13:47:55: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 13:47:55: #1 finished! INFO @ Wed, 08 Dec 2021 13:47:55: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:47:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:47:55: #2 number of paired peaks: 625 WARNING @ Wed, 08 Dec 2021 13:47:55: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Wed, 08 Dec 2021 13:47:55: start model_add_line... INFO @ Wed, 08 Dec 2021 13:47:55: start X-correlation... INFO @ Wed, 08 Dec 2021 13:47:55: end of X-cor INFO @ Wed, 08 Dec 2021 13:47:55: #2 finished! INFO @ Wed, 08 Dec 2021 13:47:55: #2 predicted fragment length is 223 bps INFO @ Wed, 08 Dec 2021 13:47:55: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 08 Dec 2021 13:47:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.05_model.r WARNING @ Wed, 08 Dec 2021 13:47:56: #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 13:47:56: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 08 Dec 2021 13:47:56: #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 13:47:56: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:47:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:48:01: 7000000 INFO @ Wed, 08 Dec 2021 13:48:02: 10000000 INFO @ Wed, 08 Dec 2021 13:48:04: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:48:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.05_peaks.xls INFO @ Wed, 08 Dec 2021 13:48:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:48:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.05_summits.bed INFO @ Wed, 08 Dec 2021 13:48:08: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (392 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:48:09: 8000000 INFO @ Wed, 08 Dec 2021 13:48:11: 11000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 13:48:17: 9000000 INFO @ Wed, 08 Dec 2021 13:48:20: 12000000 INFO @ Wed, 08 Dec 2021 13:48:24: 10000000 INFO @ Wed, 08 Dec 2021 13:48:29: 13000000 INFO @ Wed, 08 Dec 2021 13:48:29: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:48:29: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:48:29: #1 total tags in treatment: 3664643 INFO @ Wed, 08 Dec 2021 13:48:29: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:48:29: #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 13:48:29: #1 tags after filtering in treatment: 3393026 INFO @ Wed, 08 Dec 2021 13:48:29: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 13:48:29: #1 finished! INFO @ Wed, 08 Dec 2021 13:48:29: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:48:29: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:48:29: #2 number of paired peaks: 625 WARNING @ Wed, 08 Dec 2021 13:48:29: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Wed, 08 Dec 2021 13:48:29: start model_add_line... INFO @ Wed, 08 Dec 2021 13:48:29: start X-correlation... INFO @ Wed, 08 Dec 2021 13:48:29: end of X-cor INFO @ Wed, 08 Dec 2021 13:48:29: #2 finished! INFO @ Wed, 08 Dec 2021 13:48:29: #2 predicted fragment length is 223 bps INFO @ Wed, 08 Dec 2021 13:48:29: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 08 Dec 2021 13:48:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.10_model.r WARNING @ Wed, 08 Dec 2021 13:48:29: #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 13:48:29: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 08 Dec 2021 13:48:29: #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 13:48:29: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:48:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:48:32: 11000000 INFO @ Wed, 08 Dec 2021 13:48:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 13:48:39: 12000000 INFO @ Wed, 08 Dec 2021 13:48:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.10_peaks.xls INFO @ Wed, 08 Dec 2021 13:48:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:48:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.10_summits.bed INFO @ Wed, 08 Dec 2021 13:48:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (300 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:48:46: 13000000 INFO @ Wed, 08 Dec 2021 13:48:46: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 13:48:46: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 13:48:46: #1 total tags in treatment: 3664643 INFO @ Wed, 08 Dec 2021 13:48:46: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:48:46: #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 13:48:47: #1 tags after filtering in treatment: 3393026 INFO @ Wed, 08 Dec 2021 13:48:47: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 13:48:47: #1 finished! INFO @ Wed, 08 Dec 2021 13:48:47: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:48:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:48:47: #2 number of paired peaks: 625 WARNING @ Wed, 08 Dec 2021 13:48:47: Fewer paired peaks (625) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 625 pairs to build model! INFO @ Wed, 08 Dec 2021 13:48:47: start model_add_line... INFO @ Wed, 08 Dec 2021 13:48:47: start X-correlation... INFO @ Wed, 08 Dec 2021 13:48:47: end of X-cor INFO @ Wed, 08 Dec 2021 13:48:47: #2 finished! INFO @ Wed, 08 Dec 2021 13:48:47: #2 predicted fragment length is 223 bps INFO @ Wed, 08 Dec 2021 13:48:47: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 08 Dec 2021 13:48:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.20_model.r WARNING @ Wed, 08 Dec 2021 13:48:47: #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 13:48:47: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 08 Dec 2021 13:48:47: #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 13:48:47: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:48:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:48:56: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:49:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.20_peaks.xls INFO @ Wed, 08 Dec 2021 13:49:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:49:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641211/SRX10641211.20_summits.bed INFO @ Wed, 08 Dec 2021 13:49:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (208 records, 4 fields): 4 millis CompletedMACS2peakCalling