Job ID = 14160327 SRX = SRX9555450 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 25997655 spots for SRR13111101/SRR13111101.sra Written 25997655 spots for SRR13111101/SRR13111101.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160474 ("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: 00:19:09 25997655 reads; of these: 25997655 (100.00%) were paired; of these: 5137070 (19.76%) aligned concordantly 0 times 18039840 (69.39%) aligned concordantly exactly 1 time 2820745 (10.85%) aligned concordantly >1 times ---- 5137070 pairs aligned concordantly 0 times; of these: 497915 (9.69%) aligned discordantly 1 time ---- 4639155 pairs aligned 0 times concordantly or discordantly; of these: 9278310 mates make up the pairs; of these: 8672595 (93.47%) aligned 0 times 420932 (4.54%) aligned exactly 1 time 184783 (1.99%) aligned >1 times 83.32% overall alignment rate Time searching: 00:19:09 Overall time: 00:19:09 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] 2382478 / 21301573 = 0.1118 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 01:56:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.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 01:56:48: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:56:48: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:56:54: 1000000 INFO @ Thu, 09 Dec 2021 01:57:00: 2000000 INFO @ Thu, 09 Dec 2021 01:57:05: 3000000 INFO @ Thu, 09 Dec 2021 01:57:10: 4000000 INFO @ Thu, 09 Dec 2021 01:57:16: 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 @ Thu, 09 Dec 2021 01:57:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.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 01:57:18: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:57:18: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:57:23: 6000000 INFO @ Thu, 09 Dec 2021 01:57:25: 1000000 INFO @ Thu, 09 Dec 2021 01:57:30: 7000000 INFO @ Thu, 09 Dec 2021 01:57:31: 2000000 INFO @ Thu, 09 Dec 2021 01:57:36: 8000000 INFO @ Thu, 09 Dec 2021 01:57:38: 3000000 INFO @ Thu, 09 Dec 2021 01:57:43: 9000000 INFO @ Thu, 09 Dec 2021 01:57:44: 4000000 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 01:57:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.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 01:57:48: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:57:48: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:57:49: 10000000 INFO @ Thu, 09 Dec 2021 01:57:50: 5000000 INFO @ Thu, 09 Dec 2021 01:57:56: 11000000 INFO @ Thu, 09 Dec 2021 01:57:56: 1000000 INFO @ Thu, 09 Dec 2021 01:57:57: 6000000 INFO @ Thu, 09 Dec 2021 01:58:02: 12000000 INFO @ Thu, 09 Dec 2021 01:58:04: 2000000 INFO @ Thu, 09 Dec 2021 01:58:04: 7000000 INFO @ Thu, 09 Dec 2021 01:58:09: 13000000 INFO @ Thu, 09 Dec 2021 01:58:10: 8000000 INFO @ Thu, 09 Dec 2021 01:58:11: 3000000 INFO @ Thu, 09 Dec 2021 01:58:16: 14000000 INFO @ Thu, 09 Dec 2021 01:58:17: 9000000 INFO @ Thu, 09 Dec 2021 01:58:19: 4000000 INFO @ Thu, 09 Dec 2021 01:58:22: 15000000 INFO @ Thu, 09 Dec 2021 01:58:24: 10000000 INFO @ Thu, 09 Dec 2021 01:58:26: 5000000 INFO @ Thu, 09 Dec 2021 01:58:29: 16000000 INFO @ Thu, 09 Dec 2021 01:58:30: 11000000 INFO @ Thu, 09 Dec 2021 01:58:34: 6000000 INFO @ Thu, 09 Dec 2021 01:58:36: 17000000 INFO @ Thu, 09 Dec 2021 01:58:37: 12000000 INFO @ Thu, 09 Dec 2021 01:58:42: 7000000 INFO @ Thu, 09 Dec 2021 01:58:42: 18000000 INFO @ Thu, 09 Dec 2021 01:58:44: 13000000 INFO @ Thu, 09 Dec 2021 01:58:49: 19000000 INFO @ Thu, 09 Dec 2021 01:58:49: 8000000 INFO @ Thu, 09 Dec 2021 01:58:50: 14000000 INFO @ Thu, 09 Dec 2021 01:58:56: 20000000 INFO @ Thu, 09 Dec 2021 01:58:57: 9000000 INFO @ Thu, 09 Dec 2021 01:58:57: 15000000 INFO @ Thu, 09 Dec 2021 01:59:02: 21000000 INFO @ Thu, 09 Dec 2021 01:59:04: 16000000 INFO @ Thu, 09 Dec 2021 01:59:05: 10000000 INFO @ Thu, 09 Dec 2021 01:59:09: 22000000 INFO @ Thu, 09 Dec 2021 01:59:10: 17000000 INFO @ Thu, 09 Dec 2021 01:59:12: 11000000 INFO @ Thu, 09 Dec 2021 01:59:16: 23000000 INFO @ Thu, 09 Dec 2021 01:59:17: 18000000 INFO @ Thu, 09 Dec 2021 01:59:20: 12000000 INFO @ Thu, 09 Dec 2021 01:59:22: 24000000 INFO @ Thu, 09 Dec 2021 01:59:24: 19000000 INFO @ Thu, 09 Dec 2021 01:59:28: 13000000 INFO @ Thu, 09 Dec 2021 01:59:29: 25000000 INFO @ Thu, 09 Dec 2021 01:59:31: 20000000 INFO @ Thu, 09 Dec 2021 01:59:35: 14000000 INFO @ Thu, 09 Dec 2021 01:59:36: 26000000 INFO @ Thu, 09 Dec 2021 01:59:37: 21000000 INFO @ Thu, 09 Dec 2021 01:59:42: 27000000 INFO @ Thu, 09 Dec 2021 01:59:43: 15000000 INFO @ Thu, 09 Dec 2021 01:59:44: 22000000 INFO @ Thu, 09 Dec 2021 01:59:49: 28000000 INFO @ Thu, 09 Dec 2021 01:59:51: 23000000 INFO @ Thu, 09 Dec 2021 01:59:51: 16000000 INFO @ Thu, 09 Dec 2021 01:59:56: 29000000 INFO @ Thu, 09 Dec 2021 01:59:57: 24000000 INFO @ Thu, 09 Dec 2021 01:59:58: 17000000 INFO @ Thu, 09 Dec 2021 02:00:02: 30000000 INFO @ Thu, 09 Dec 2021 02:00:04: 25000000 INFO @ Thu, 09 Dec 2021 02:00:06: 18000000 INFO @ Thu, 09 Dec 2021 02:00:09: 31000000 INFO @ Thu, 09 Dec 2021 02:00:11: 26000000 INFO @ Thu, 09 Dec 2021 02:00:14: 19000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 02:00:16: 32000000 INFO @ Thu, 09 Dec 2021 02:00:17: 27000000 INFO @ Thu, 09 Dec 2021 02:00:21: 20000000 INFO @ Thu, 09 Dec 2021 02:00:22: 33000000 INFO @ Thu, 09 Dec 2021 02:00:24: 28000000 INFO @ Thu, 09 Dec 2021 02:00:29: 21000000 INFO @ Thu, 09 Dec 2021 02:00:29: 34000000 INFO @ Thu, 09 Dec 2021 02:00:31: 29000000 INFO @ Thu, 09 Dec 2021 02:00:36: 35000000 INFO @ Thu, 09 Dec 2021 02:00:37: 22000000 INFO @ Thu, 09 Dec 2021 02:00:37: 30000000 INFO @ Thu, 09 Dec 2021 02:00:42: 36000000 INFO @ Thu, 09 Dec 2021 02:00:44: 31000000 INFO @ Thu, 09 Dec 2021 02:00:44: 23000000 INFO @ Thu, 09 Dec 2021 02:00:49: 37000000 INFO @ Thu, 09 Dec 2021 02:00:51: 32000000 INFO @ Thu, 09 Dec 2021 02:00:52: 24000000 INFO @ Thu, 09 Dec 2021 02:00:56: 38000000 INFO @ Thu, 09 Dec 2021 02:00:57: 33000000 INFO @ Thu, 09 Dec 2021 02:00:59: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 02:00:59: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 02:00:59: #1 total tags in treatment: 18499771 INFO @ Thu, 09 Dec 2021 02:00:59: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:00:59: #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 02:01:00: 25000000 INFO @ Thu, 09 Dec 2021 02:01:00: #1 tags after filtering in treatment: 16934470 INFO @ Thu, 09 Dec 2021 02:01:00: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 09 Dec 2021 02:01:00: #1 finished! INFO @ Thu, 09 Dec 2021 02:01:00: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:01:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:01:01: #2 number of paired peaks: 305 WARNING @ Thu, 09 Dec 2021 02:01:01: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Thu, 09 Dec 2021 02:01:01: start model_add_line... INFO @ Thu, 09 Dec 2021 02:01:01: start X-correlation... INFO @ Thu, 09 Dec 2021 02:01:01: end of X-cor INFO @ Thu, 09 Dec 2021 02:01:01: #2 finished! INFO @ Thu, 09 Dec 2021 02:01:01: #2 predicted fragment length is 105 bps INFO @ Thu, 09 Dec 2021 02:01:01: #2 alternative fragment length(s) may be 3,105,121 bps INFO @ Thu, 09 Dec 2021 02:01:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.05_model.r INFO @ Thu, 09 Dec 2021 02:01:01: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:01:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:01:04: 34000000 INFO @ Thu, 09 Dec 2021 02:01:07: 26000000 INFO @ Thu, 09 Dec 2021 02:01:10: 35000000 INFO @ Thu, 09 Dec 2021 02:01:15: 27000000 INFO @ Thu, 09 Dec 2021 02:01:17: 36000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 02:01:22: 28000000 INFO @ Thu, 09 Dec 2021 02:01:23: 37000000 INFO @ Thu, 09 Dec 2021 02:01:30: 38000000 INFO @ Thu, 09 Dec 2021 02:01:30: 29000000 INFO @ Thu, 09 Dec 2021 02:01:30: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:01:34: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 02:01:34: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 02:01:34: #1 total tags in treatment: 18499771 INFO @ Thu, 09 Dec 2021 02:01:34: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:01:34: #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 02:01:34: #1 tags after filtering in treatment: 16934470 INFO @ Thu, 09 Dec 2021 02:01:34: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 09 Dec 2021 02:01:34: #1 finished! INFO @ Thu, 09 Dec 2021 02:01:34: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:01:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:01:35: #2 number of paired peaks: 305 WARNING @ Thu, 09 Dec 2021 02:01:35: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Thu, 09 Dec 2021 02:01:35: start model_add_line... INFO @ Thu, 09 Dec 2021 02:01:35: start X-correlation... INFO @ Thu, 09 Dec 2021 02:01:35: end of X-cor INFO @ Thu, 09 Dec 2021 02:01:35: #2 finished! INFO @ Thu, 09 Dec 2021 02:01:35: #2 predicted fragment length is 105 bps INFO @ Thu, 09 Dec 2021 02:01:35: #2 alternative fragment length(s) may be 3,105,121 bps INFO @ Thu, 09 Dec 2021 02:01:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.10_model.r INFO @ Thu, 09 Dec 2021 02:01:35: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:01:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:01:37: 30000000 INFO @ Thu, 09 Dec 2021 02:01:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.05_peaks.xls INFO @ Thu, 09 Dec 2021 02:01:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:01:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.05_summits.bed INFO @ Thu, 09 Dec 2021 02:01:44: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (469 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:01:44: 31000000 INFO @ Thu, 09 Dec 2021 02:01:51: 32000000 INFO @ Thu, 09 Dec 2021 02:01:58: 33000000 INFO @ Thu, 09 Dec 2021 02:02:05: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:02:05: 34000000 INFO @ Thu, 09 Dec 2021 02:02:12: 35000000 INFO @ Thu, 09 Dec 2021 02:02:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.10_peaks.xls INFO @ Thu, 09 Dec 2021 02:02:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:02:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.10_summits.bed INFO @ Thu, 09 Dec 2021 02:02:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (355 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 02:02:19: 36000000 INFO @ Thu, 09 Dec 2021 02:02:26: 37000000 INFO @ Thu, 09 Dec 2021 02:02:33: 38000000 INFO @ Thu, 09 Dec 2021 02:02:37: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 02:02:37: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 02:02:37: #1 total tags in treatment: 18499771 INFO @ Thu, 09 Dec 2021 02:02:37: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 02:02:37: #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 02:02:37: #1 tags after filtering in treatment: 16934470 INFO @ Thu, 09 Dec 2021 02:02:37: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 09 Dec 2021 02:02:37: #1 finished! INFO @ Thu, 09 Dec 2021 02:02:37: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 02:02:37: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 02:02:38: #2 number of paired peaks: 305 WARNING @ Thu, 09 Dec 2021 02:02:38: Fewer paired peaks (305) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 305 pairs to build model! INFO @ Thu, 09 Dec 2021 02:02:38: start model_add_line... INFO @ Thu, 09 Dec 2021 02:02:38: start X-correlation... INFO @ Thu, 09 Dec 2021 02:02:38: end of X-cor INFO @ Thu, 09 Dec 2021 02:02:38: #2 finished! INFO @ Thu, 09 Dec 2021 02:02:38: #2 predicted fragment length is 105 bps INFO @ Thu, 09 Dec 2021 02:02:38: #2 alternative fragment length(s) may be 3,105,121 bps INFO @ Thu, 09 Dec 2021 02:02:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.20_model.r INFO @ Thu, 09 Dec 2021 02:02:38: #3 Call peaks... INFO @ Thu, 09 Dec 2021 02:02:38: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 02:03:08: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 02:03:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.20_peaks.xls INFO @ Thu, 09 Dec 2021 02:03:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 02:03:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9555450/SRX9555450.20_summits.bed INFO @ Thu, 09 Dec 2021 02:03:21: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (212 records, 4 fields): 1 millis CompletedMACS2peakCalling