Job ID = 14160371 SRX = SRX9567187 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 28561580 spots for SRR13125162/SRR13125162.sra Written 28561580 spots for SRR13125162/SRR13125162.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160626 ("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: 00:58:27 28561580 reads; of these: 28561580 (100.00%) were paired; of these: 8513047 (29.81%) aligned concordantly 0 times 17340226 (60.71%) aligned concordantly exactly 1 time 2708307 (9.48%) aligned concordantly >1 times ---- 8513047 pairs aligned concordantly 0 times; of these: 6113446 (71.81%) aligned discordantly 1 time ---- 2399601 pairs aligned 0 times concordantly or discordantly; of these: 4799202 mates make up the pairs; of these: 1998801 (41.65%) aligned 0 times 1375070 (28.65%) aligned exactly 1 time 1425331 (29.70%) aligned >1 times 96.50% overall alignment rate Time searching: 00:58:27 Overall time: 00:58:27 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 40 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] 17969486 / 26137152 = 0.6875 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 @ Thu, 09 Dec 2021 03:09:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.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 @ Thu, 09 Dec 2021 03:09:13: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:09:13: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:09:20: 1000000 INFO @ Thu, 09 Dec 2021 03:09:27: 2000000 INFO @ Thu, 09 Dec 2021 03:09:34: 3000000 INFO @ Thu, 09 Dec 2021 03:09:41: 4000000 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 @ Thu, 09 Dec 2021 03:09:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.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 @ Thu, 09 Dec 2021 03:09:43: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:09:43: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:09:48: 5000000 INFO @ Thu, 09 Dec 2021 03:09:51: 1000000 INFO @ Thu, 09 Dec 2021 03:09:56: 6000000 INFO @ Thu, 09 Dec 2021 03:09:59: 2000000 INFO @ Thu, 09 Dec 2021 03:10:04: 7000000 INFO @ Thu, 09 Dec 2021 03:10:07: 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 @ Thu, 09 Dec 2021 03:10:12: 8000000 INFO @ Thu, 09 Dec 2021 03:10:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.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 @ Thu, 09 Dec 2021 03:10:13: #1 read tag files... INFO @ Thu, 09 Dec 2021 03:10:13: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 03:10:14: 4000000 INFO @ Thu, 09 Dec 2021 03:10:20: 9000000 INFO @ Thu, 09 Dec 2021 03:10:21: 1000000 INFO @ Thu, 09 Dec 2021 03:10:22: 5000000 INFO @ Thu, 09 Dec 2021 03:10:27: 10000000 INFO @ Thu, 09 Dec 2021 03:10:29: 2000000 INFO @ Thu, 09 Dec 2021 03:10:30: 6000000 INFO @ Thu, 09 Dec 2021 03:10:36: 11000000 INFO @ Thu, 09 Dec 2021 03:10:37: 3000000 INFO @ Thu, 09 Dec 2021 03:10:38: 7000000 INFO @ Thu, 09 Dec 2021 03:10:44: 12000000 INFO @ Thu, 09 Dec 2021 03:10:45: 4000000 INFO @ Thu, 09 Dec 2021 03:10:46: 8000000 INFO @ Thu, 09 Dec 2021 03:10:52: 13000000 INFO @ Thu, 09 Dec 2021 03:10:53: 5000000 INFO @ Thu, 09 Dec 2021 03:10:54: 9000000 INFO @ Thu, 09 Dec 2021 03:11:00: 14000000 INFO @ Thu, 09 Dec 2021 03:11:01: 6000000 INFO @ Thu, 09 Dec 2021 03:11:03: 10000000 INFO @ Thu, 09 Dec 2021 03:11:08: 15000000 INFO @ Thu, 09 Dec 2021 03:11:09: 7000000 INFO @ Thu, 09 Dec 2021 03:11:11: 11000000 INFO @ Thu, 09 Dec 2021 03:11:16: 16000000 INFO @ Thu, 09 Dec 2021 03:11:17: 8000000 INFO @ Thu, 09 Dec 2021 03:11:19: 12000000 INFO @ Thu, 09 Dec 2021 03:11:24: 17000000 INFO @ Thu, 09 Dec 2021 03:11:25: 9000000 INFO @ Thu, 09 Dec 2021 03:11:26: 13000000 INFO @ Thu, 09 Dec 2021 03:11:32: 18000000 INFO @ Thu, 09 Dec 2021 03:11:33: 10000000 INFO @ Thu, 09 Dec 2021 03:11:34: 14000000 INFO @ Thu, 09 Dec 2021 03:11:39: 19000000 INFO @ Thu, 09 Dec 2021 03:11:40: 11000000 INFO @ Thu, 09 Dec 2021 03:11:41: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:11:41: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:11:41: #1 total tags in treatment: 6376467 INFO @ Thu, 09 Dec 2021 03:11:41: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:11:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:11:41: #1 tags after filtering in treatment: 5790882 INFO @ Thu, 09 Dec 2021 03:11:41: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 09 Dec 2021 03:11:41: #1 finished! INFO @ Thu, 09 Dec 2021 03:11:41: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:11:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:11:41: #2 number of paired peaks: 599 WARNING @ Thu, 09 Dec 2021 03:11:41: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Thu, 09 Dec 2021 03:11:41: start model_add_line... INFO @ Thu, 09 Dec 2021 03:11:41: start X-correlation... INFO @ Thu, 09 Dec 2021 03:11:41: end of X-cor INFO @ Thu, 09 Dec 2021 03:11:41: #2 finished! INFO @ Thu, 09 Dec 2021 03:11:41: #2 predicted fragment length is 225 bps INFO @ Thu, 09 Dec 2021 03:11:41: #2 alternative fragment length(s) may be 225 bps INFO @ Thu, 09 Dec 2021 03:11:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.05_model.r WARNING @ Thu, 09 Dec 2021 03:11:41: #2 Since the d (225) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:11:41: #2 You may need to consider one of the other alternative d(s): 225 WARNING @ Thu, 09 Dec 2021 03:11:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:11:41: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:11:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:11:42: 15000000 INFO @ Thu, 09 Dec 2021 03:11:48: 12000000 INFO @ Thu, 09 Dec 2021 03:11:50: 16000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 03:11:55: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:11:56: 13000000 INFO @ Thu, 09 Dec 2021 03:11:58: 17000000 INFO @ Thu, 09 Dec 2021 03:12:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.05_peaks.xls INFO @ Thu, 09 Dec 2021 03:12:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:12:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.05_summits.bed INFO @ Thu, 09 Dec 2021 03:12:01: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (482 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:12:04: 14000000 INFO @ Thu, 09 Dec 2021 03:12:06: 18000000 INFO @ Thu, 09 Dec 2021 03:12:12: 15000000 INFO @ Thu, 09 Dec 2021 03:12:14: 19000000 INFO @ Thu, 09 Dec 2021 03:12:16: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:12:16: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:12:16: #1 total tags in treatment: 6376467 INFO @ Thu, 09 Dec 2021 03:12:16: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:12:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:12:16: #1 tags after filtering in treatment: 5790882 INFO @ Thu, 09 Dec 2021 03:12:16: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 09 Dec 2021 03:12:16: #1 finished! INFO @ Thu, 09 Dec 2021 03:12:16: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:12:16: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:12:16: #2 number of paired peaks: 599 WARNING @ Thu, 09 Dec 2021 03:12:16: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Thu, 09 Dec 2021 03:12:16: start model_add_line... INFO @ Thu, 09 Dec 2021 03:12:16: start X-correlation... INFO @ Thu, 09 Dec 2021 03:12:16: end of X-cor INFO @ Thu, 09 Dec 2021 03:12:16: #2 finished! INFO @ Thu, 09 Dec 2021 03:12:16: #2 predicted fragment length is 225 bps INFO @ Thu, 09 Dec 2021 03:12:16: #2 alternative fragment length(s) may be 225 bps INFO @ Thu, 09 Dec 2021 03:12:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.10_model.r WARNING @ Thu, 09 Dec 2021 03:12:16: #2 Since the d (225) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:12:16: #2 You may need to consider one of the other alternative d(s): 225 WARNING @ Thu, 09 Dec 2021 03:12:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:12:16: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:12:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:12:20: 16000000 INFO @ Thu, 09 Dec 2021 03:12:27: 17000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 03:12:30: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:12:34: 18000000 INFO @ Thu, 09 Dec 2021 03:12:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.10_peaks.xls INFO @ Thu, 09 Dec 2021 03:12:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:12:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.10_summits.bed INFO @ Thu, 09 Dec 2021 03:12:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (365 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 03:12:42: 19000000 INFO @ Thu, 09 Dec 2021 03:12:43: #1 tag size is determined as 151 bps INFO @ Thu, 09 Dec 2021 03:12:43: #1 tag size = 151 INFO @ Thu, 09 Dec 2021 03:12:43: #1 total tags in treatment: 6376467 INFO @ Thu, 09 Dec 2021 03:12:43: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 03:12:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 03:12:43: #1 tags after filtering in treatment: 5790882 INFO @ Thu, 09 Dec 2021 03:12:43: #1 Redundant rate of treatment: 0.09 INFO @ Thu, 09 Dec 2021 03:12:43: #1 finished! INFO @ Thu, 09 Dec 2021 03:12:43: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 03:12:43: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 03:12:43: #2 number of paired peaks: 599 WARNING @ Thu, 09 Dec 2021 03:12:43: Fewer paired peaks (599) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 599 pairs to build model! INFO @ Thu, 09 Dec 2021 03:12:43: start model_add_line... INFO @ Thu, 09 Dec 2021 03:12:43: start X-correlation... INFO @ Thu, 09 Dec 2021 03:12:43: end of X-cor INFO @ Thu, 09 Dec 2021 03:12:43: #2 finished! INFO @ Thu, 09 Dec 2021 03:12:43: #2 predicted fragment length is 225 bps INFO @ Thu, 09 Dec 2021 03:12:43: #2 alternative fragment length(s) may be 225 bps INFO @ Thu, 09 Dec 2021 03:12:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.20_model.r WARNING @ Thu, 09 Dec 2021 03:12:43: #2 Since the d (225) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 09 Dec 2021 03:12:43: #2 You may need to consider one of the other alternative d(s): 225 WARNING @ Thu, 09 Dec 2021 03:12:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 09 Dec 2021 03:12:43: #3 Call peaks... INFO @ Thu, 09 Dec 2021 03:12:43: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 03:12:57: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 03:13:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.20_peaks.xls INFO @ Thu, 09 Dec 2021 03:13:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 03:13:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9567187/SRX9567187.20_summits.bed INFO @ Thu, 09 Dec 2021 03:13:03: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (259 records, 4 fields): 2 millis CompletedMACS2peakCalling