Job ID = 14158273 SRX = SRX10342588 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 11220938 spots for SRR13964632/SRR13964632.sra Written 11220938 spots for SRR13964632/SRR13964632.sra Read 12241347 spots for SRR13964633/SRR13964633.sra Written 12241347 spots for SRR13964633/SRR13964633.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158830 ("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: 00:18:01 23462285 reads; of these: 23462285 (100.00%) were paired; of these: 8308647 (35.41%) aligned concordantly 0 times 12590229 (53.66%) aligned concordantly exactly 1 time 2563409 (10.93%) aligned concordantly >1 times ---- 8308647 pairs aligned concordantly 0 times; of these: 5801469 (69.82%) aligned discordantly 1 time ---- 2507178 pairs aligned 0 times concordantly or discordantly; of these: 5014356 mates make up the pairs; of these: 2664946 (53.15%) aligned 0 times 918170 (18.31%) aligned exactly 1 time 1431240 (28.54%) aligned >1 times 94.32% overall alignment rate Time searching: 00:18:01 Overall time: 00:18:01 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] 5754835 / 20944861 = 0.2748 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 16:06:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.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 16:06:31: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:06:31: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:06:37: 1000000 INFO @ Wed, 08 Dec 2021 16:06:42: 2000000 INFO @ Wed, 08 Dec 2021 16:06:47: 3000000 INFO @ Wed, 08 Dec 2021 16:06:52: 4000000 INFO @ Wed, 08 Dec 2021 16:06:57: 5000000 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 16:07:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.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 16:07:01: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:07:01: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:07:02: 6000000 INFO @ Wed, 08 Dec 2021 16:07:06: 1000000 INFO @ Wed, 08 Dec 2021 16:07:08: 7000000 INFO @ Wed, 08 Dec 2021 16:07:10: 2000000 INFO @ Wed, 08 Dec 2021 16:07:13: 8000000 INFO @ Wed, 08 Dec 2021 16:07:15: 3000000 INFO @ Wed, 08 Dec 2021 16:07:19: 9000000 INFO @ Wed, 08 Dec 2021 16:07:19: 4000000 INFO @ Wed, 08 Dec 2021 16:07:24: 5000000 INFO @ Wed, 08 Dec 2021 16:07:24: 10000000 INFO @ Wed, 08 Dec 2021 16:07:29: 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 16:07:30: 11000000 INFO @ Wed, 08 Dec 2021 16:07:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.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 16:07:31: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:07:31: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:07:33: 7000000 INFO @ Wed, 08 Dec 2021 16:07:35: 12000000 INFO @ Wed, 08 Dec 2021 16:07:36: 1000000 INFO @ Wed, 08 Dec 2021 16:07:38: 8000000 INFO @ Wed, 08 Dec 2021 16:07:40: 2000000 INFO @ Wed, 08 Dec 2021 16:07:41: 13000000 INFO @ Wed, 08 Dec 2021 16:07:43: 9000000 INFO @ Wed, 08 Dec 2021 16:07:45: 3000000 INFO @ Wed, 08 Dec 2021 16:07:46: 14000000 INFO @ Wed, 08 Dec 2021 16:07:48: 10000000 INFO @ Wed, 08 Dec 2021 16:07:50: 4000000 INFO @ Wed, 08 Dec 2021 16:07:52: 15000000 INFO @ Wed, 08 Dec 2021 16:07:52: 11000000 INFO @ Wed, 08 Dec 2021 16:07:54: 5000000 INFO @ Wed, 08 Dec 2021 16:07:57: 12000000 INFO @ Wed, 08 Dec 2021 16:07:57: 16000000 INFO @ Wed, 08 Dec 2021 16:07:59: 6000000 INFO @ Wed, 08 Dec 2021 16:08:02: 13000000 INFO @ Wed, 08 Dec 2021 16:08:03: 17000000 INFO @ Wed, 08 Dec 2021 16:08:04: 7000000 INFO @ Wed, 08 Dec 2021 16:08:07: 14000000 INFO @ Wed, 08 Dec 2021 16:08:08: 18000000 INFO @ Wed, 08 Dec 2021 16:08:09: 8000000 INFO @ Wed, 08 Dec 2021 16:08:11: 15000000 INFO @ Wed, 08 Dec 2021 16:08:13: 9000000 INFO @ Wed, 08 Dec 2021 16:08:14: 19000000 INFO @ Wed, 08 Dec 2021 16:08:16: 16000000 INFO @ Wed, 08 Dec 2021 16:08:18: 10000000 INFO @ Wed, 08 Dec 2021 16:08:19: 20000000 INFO @ Wed, 08 Dec 2021 16:08:21: 17000000 INFO @ Wed, 08 Dec 2021 16:08:23: 11000000 INFO @ Wed, 08 Dec 2021 16:08:25: 21000000 INFO @ Wed, 08 Dec 2021 16:08:25: 18000000 INFO @ Wed, 08 Dec 2021 16:08:28: 12000000 INFO @ Wed, 08 Dec 2021 16:08:30: 22000000 INFO @ Wed, 08 Dec 2021 16:08:30: 19000000 INFO @ Wed, 08 Dec 2021 16:08:32: 13000000 INFO @ Wed, 08 Dec 2021 16:08:35: 20000000 INFO @ Wed, 08 Dec 2021 16:08:35: 23000000 INFO @ Wed, 08 Dec 2021 16:08:37: 14000000 INFO @ Wed, 08 Dec 2021 16:08:40: 21000000 INFO @ Wed, 08 Dec 2021 16:08:41: 24000000 INFO @ Wed, 08 Dec 2021 16:08:42: 15000000 INFO @ Wed, 08 Dec 2021 16:08:44: 22000000 INFO @ Wed, 08 Dec 2021 16:08:46: 25000000 INFO @ Wed, 08 Dec 2021 16:08:46: 16000000 INFO @ Wed, 08 Dec 2021 16:08:49: 23000000 INFO @ Wed, 08 Dec 2021 16:08:51: 17000000 INFO @ Wed, 08 Dec 2021 16:08:52: 26000000 INFO @ Wed, 08 Dec 2021 16:08:54: 24000000 INFO @ Wed, 08 Dec 2021 16:08:56: 18000000 INFO @ Wed, 08 Dec 2021 16:08:57: 27000000 INFO @ Wed, 08 Dec 2021 16:08:59: 25000000 INFO @ Wed, 08 Dec 2021 16:09:00: 19000000 INFO @ Wed, 08 Dec 2021 16:09:03: 28000000 INFO @ Wed, 08 Dec 2021 16:09:03: 26000000 INFO @ Wed, 08 Dec 2021 16:09:05: 20000000 INFO @ Wed, 08 Dec 2021 16:09:08: 29000000 INFO @ Wed, 08 Dec 2021 16:09:08: 27000000 INFO @ Wed, 08 Dec 2021 16:09:10: 21000000 INFO @ Wed, 08 Dec 2021 16:09:13: 28000000 INFO @ Wed, 08 Dec 2021 16:09:13: 30000000 INFO @ Wed, 08 Dec 2021 16:09:15: 22000000 INFO @ Wed, 08 Dec 2021 16:09:18: 29000000 INFO @ Wed, 08 Dec 2021 16:09:19: 31000000 INFO @ Wed, 08 Dec 2021 16:09:19: 23000000 INFO @ Wed, 08 Dec 2021 16:09:22: 30000000 INFO @ Wed, 08 Dec 2021 16:09:24: 24000000 INFO @ Wed, 08 Dec 2021 16:09:24: 32000000 INFO @ Wed, 08 Dec 2021 16:09:27: 31000000 INFO @ Wed, 08 Dec 2021 16:09:28: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:09:28: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:09:28: #1 total tags in treatment: 10677344 INFO @ Wed, 08 Dec 2021 16:09:28: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:09:28: #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 16:09:28: #1 tags after filtering in treatment: 9550458 INFO @ Wed, 08 Dec 2021 16:09:28: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 08 Dec 2021 16:09:28: #1 finished! INFO @ Wed, 08 Dec 2021 16:09:28: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:09:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:09:29: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 16:09:29: #2 number of paired peaks: 680 WARNING @ Wed, 08 Dec 2021 16:09:29: Fewer paired peaks (680) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 680 pairs to build model! INFO @ Wed, 08 Dec 2021 16:09:29: start model_add_line... INFO @ Wed, 08 Dec 2021 16:09:29: start X-correlation... INFO @ Wed, 08 Dec 2021 16:09:29: end of X-cor INFO @ Wed, 08 Dec 2021 16:09:29: #2 finished! INFO @ Wed, 08 Dec 2021 16:09:29: #2 predicted fragment length is 111 bps INFO @ Wed, 08 Dec 2021 16:09:29: #2 alternative fragment length(s) may be 4,111,116 bps INFO @ Wed, 08 Dec 2021 16:09:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.05_model.r INFO @ Wed, 08 Dec 2021 16:09:29: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:09:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:09:32: 32000000 INFO @ Wed, 08 Dec 2021 16:09:33: 26000000 INFO @ Wed, 08 Dec 2021 16:09:35: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:09:35: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:09:35: #1 total tags in treatment: 10677344 INFO @ Wed, 08 Dec 2021 16:09:35: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:09:35: #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 16:09:35: #1 tags after filtering in treatment: 9550458 INFO @ Wed, 08 Dec 2021 16:09:35: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 08 Dec 2021 16:09:35: #1 finished! INFO @ Wed, 08 Dec 2021 16:09:35: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:09:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:09:36: #2 number of paired peaks: 680 WARNING @ Wed, 08 Dec 2021 16:09:36: Fewer paired peaks (680) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 680 pairs to build model! INFO @ Wed, 08 Dec 2021 16:09:36: start model_add_line... INFO @ Wed, 08 Dec 2021 16:09:36: start X-correlation... INFO @ Wed, 08 Dec 2021 16:09:36: end of X-cor INFO @ Wed, 08 Dec 2021 16:09:36: #2 finished! INFO @ Wed, 08 Dec 2021 16:09:36: #2 predicted fragment length is 111 bps INFO @ Wed, 08 Dec 2021 16:09:36: #2 alternative fragment length(s) may be 4,111,116 bps INFO @ Wed, 08 Dec 2021 16:09:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.10_model.r INFO @ Wed, 08 Dec 2021 16:09:36: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:09:36: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:09:38: 27000000 INFO @ Wed, 08 Dec 2021 16:09:42: 28000000 INFO @ Wed, 08 Dec 2021 16:09:46: 29000000 INFO @ Wed, 08 Dec 2021 16:09:48: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:09:51: 30000000 INFO @ Wed, 08 Dec 2021 16:09:54: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:09:55: 31000000 INFO @ Wed, 08 Dec 2021 16:09:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.05_peaks.xls INFO @ Wed, 08 Dec 2021 16:09:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:09:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.05_summits.bed INFO @ Wed, 08 Dec 2021 16:09:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (539 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:10:00: 32000000 INFO @ Wed, 08 Dec 2021 16:10:03: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:10:03: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:10:03: #1 total tags in treatment: 10677344 INFO @ Wed, 08 Dec 2021 16:10:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:10:03: #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 16:10:03: #1 tags after filtering in treatment: 9550458 INFO @ Wed, 08 Dec 2021 16:10:03: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 08 Dec 2021 16:10:03: #1 finished! INFO @ Wed, 08 Dec 2021 16:10:03: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:10:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:10:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.10_peaks.xls INFO @ Wed, 08 Dec 2021 16:10:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:10:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.10_summits.bed INFO @ Wed, 08 Dec 2021 16:10:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (410 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:10:04: #2 number of paired peaks: 680 WARNING @ Wed, 08 Dec 2021 16:10:04: Fewer paired peaks (680) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 680 pairs to build model! INFO @ Wed, 08 Dec 2021 16:10:04: start model_add_line... INFO @ Wed, 08 Dec 2021 16:10:04: start X-correlation... INFO @ Wed, 08 Dec 2021 16:10:04: end of X-cor INFO @ Wed, 08 Dec 2021 16:10:04: #2 finished! INFO @ Wed, 08 Dec 2021 16:10:04: #2 predicted fragment length is 111 bps INFO @ Wed, 08 Dec 2021 16:10:04: #2 alternative fragment length(s) may be 4,111,116 bps INFO @ Wed, 08 Dec 2021 16:10:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.20_model.r INFO @ Wed, 08 Dec 2021 16:10:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:10:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:10:23: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 16:10:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.20_peaks.xls INFO @ Wed, 08 Dec 2021 16:10:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:10:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342588/SRX10342588.20_summits.bed INFO @ Wed, 08 Dec 2021 16:10:32: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (259 records, 4 fields): 2 millis CompletedMACS2peakCalling