Job ID = 14158910 SRX = SRX8976714 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14275919 spots for SRR12483318/SRR12483318.sra Written 14275919 spots for SRR12483318/SRR12483318.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159261 ("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: 00:11:15 14275919 reads; of these: 14275919 (100.00%) were paired; of these: 226071 (1.58%) aligned concordantly 0 times 12188813 (85.38%) aligned concordantly exactly 1 time 1861035 (13.04%) aligned concordantly >1 times ---- 226071 pairs aligned concordantly 0 times; of these: 79382 (35.11%) aligned discordantly 1 time ---- 146689 pairs aligned 0 times concordantly or discordantly; of these: 293378 mates make up the pairs; of these: 188068 (64.10%) aligned 0 times 66750 (22.75%) aligned exactly 1 time 38560 (13.14%) aligned >1 times 99.34% overall alignment rate Time searching: 00:11:15 Overall time: 00:11:15 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] 203007 / 14111791 = 0.0144 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 18:36:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.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 18:36:59: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:36:59: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:37:04: 1000000 INFO @ Wed, 08 Dec 2021 18:37:10: 2000000 INFO @ Wed, 08 Dec 2021 18:37:15: 3000000 INFO @ Wed, 08 Dec 2021 18:37:20: 4000000 INFO @ Wed, 08 Dec 2021 18:37:25: 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 18:37:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.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 18:37:29: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:37:29: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:37:30: 6000000 INFO @ Wed, 08 Dec 2021 18:37:36: 1000000 INFO @ Wed, 08 Dec 2021 18:37:37: 7000000 INFO @ Wed, 08 Dec 2021 18:37:44: 8000000 INFO @ Wed, 08 Dec 2021 18:37:44: 2000000 INFO @ Wed, 08 Dec 2021 18:37:50: 9000000 INFO @ Wed, 08 Dec 2021 18:37:51: 3000000 INFO @ Wed, 08 Dec 2021 18:37:57: 10000000 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 18:37:58: 4000000 INFO @ Wed, 08 Dec 2021 18:37:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.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 18:37:59: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:37:59: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:38:03: 11000000 INFO @ Wed, 08 Dec 2021 18:38:06: 5000000 INFO @ Wed, 08 Dec 2021 18:38:06: 1000000 INFO @ Wed, 08 Dec 2021 18:38:10: 12000000 INFO @ Wed, 08 Dec 2021 18:38:13: 6000000 INFO @ Wed, 08 Dec 2021 18:38:14: 2000000 INFO @ Wed, 08 Dec 2021 18:38:17: 13000000 INFO @ Wed, 08 Dec 2021 18:38:21: 7000000 INFO @ Wed, 08 Dec 2021 18:38:21: 3000000 INFO @ Wed, 08 Dec 2021 18:38:24: 14000000 INFO @ Wed, 08 Dec 2021 18:38:28: 8000000 INFO @ Wed, 08 Dec 2021 18:38:28: 4000000 INFO @ Wed, 08 Dec 2021 18:38:30: 15000000 INFO @ Wed, 08 Dec 2021 18:38:36: 5000000 INFO @ Wed, 08 Dec 2021 18:38:36: 9000000 INFO @ Wed, 08 Dec 2021 18:38:37: 16000000 INFO @ Wed, 08 Dec 2021 18:38:43: 10000000 INFO @ Wed, 08 Dec 2021 18:38:43: 6000000 INFO @ Wed, 08 Dec 2021 18:38:44: 17000000 INFO @ Wed, 08 Dec 2021 18:38:50: 18000000 INFO @ Wed, 08 Dec 2021 18:38:50: 11000000 INFO @ Wed, 08 Dec 2021 18:38:51: 7000000 INFO @ Wed, 08 Dec 2021 18:38:57: 19000000 INFO @ Wed, 08 Dec 2021 18:38:58: 12000000 INFO @ Wed, 08 Dec 2021 18:38:58: 8000000 INFO @ Wed, 08 Dec 2021 18:39:04: 20000000 INFO @ Wed, 08 Dec 2021 18:39:05: 13000000 INFO @ Wed, 08 Dec 2021 18:39:06: 9000000 INFO @ Wed, 08 Dec 2021 18:39:10: 21000000 INFO @ Wed, 08 Dec 2021 18:39:13: 14000000 INFO @ Wed, 08 Dec 2021 18:39:13: 10000000 INFO @ Wed, 08 Dec 2021 18:39:17: 22000000 INFO @ Wed, 08 Dec 2021 18:39:20: 15000000 INFO @ Wed, 08 Dec 2021 18:39:20: 11000000 INFO @ Wed, 08 Dec 2021 18:39:24: 23000000 INFO @ Wed, 08 Dec 2021 18:39:28: 16000000 INFO @ Wed, 08 Dec 2021 18:39:28: 12000000 INFO @ Wed, 08 Dec 2021 18:39:31: 24000000 INFO @ Wed, 08 Dec 2021 18:39:35: 17000000 INFO @ Wed, 08 Dec 2021 18:39:35: 13000000 INFO @ Wed, 08 Dec 2021 18:39:37: 25000000 INFO @ Wed, 08 Dec 2021 18:39:43: 18000000 INFO @ Wed, 08 Dec 2021 18:39:43: 14000000 INFO @ Wed, 08 Dec 2021 18:39:44: 26000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:39:50: 19000000 INFO @ Wed, 08 Dec 2021 18:39:50: 15000000 INFO @ Wed, 08 Dec 2021 18:39:51: 27000000 INFO @ Wed, 08 Dec 2021 18:39:57: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:39:57: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:39:57: #1 total tags in treatment: 13847430 INFO @ Wed, 08 Dec 2021 18:39:57: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:39:57: #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 18:39:57: #1 tags after filtering in treatment: 12925039 INFO @ Wed, 08 Dec 2021 18:39:57: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:39:57: #1 finished! INFO @ Wed, 08 Dec 2021 18:39:57: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:39:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:39:58: 16000000 INFO @ Wed, 08 Dec 2021 18:39:58: 20000000 INFO @ Wed, 08 Dec 2021 18:39:58: #2 number of paired peaks: 304 WARNING @ Wed, 08 Dec 2021 18:39:58: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Wed, 08 Dec 2021 18:39:58: start model_add_line... INFO @ Wed, 08 Dec 2021 18:39:58: start X-correlation... INFO @ Wed, 08 Dec 2021 18:39:58: end of X-cor INFO @ Wed, 08 Dec 2021 18:39:58: #2 finished! INFO @ Wed, 08 Dec 2021 18:39:58: #2 predicted fragment length is 153 bps INFO @ Wed, 08 Dec 2021 18:39:58: #2 alternative fragment length(s) may be 4,153 bps INFO @ Wed, 08 Dec 2021 18:39:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.05_model.r INFO @ Wed, 08 Dec 2021 18:39:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:39:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:40:05: 17000000 INFO @ Wed, 08 Dec 2021 18:40:05: 21000000 INFO @ Wed, 08 Dec 2021 18:40:12: 18000000 INFO @ Wed, 08 Dec 2021 18:40:13: 22000000 INFO @ Wed, 08 Dec 2021 18:40:19: 19000000 INFO @ Wed, 08 Dec 2021 18:40:20: 23000000 INFO @ Wed, 08 Dec 2021 18:40:23: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:40:27: 20000000 INFO @ Wed, 08 Dec 2021 18:40:27: 24000000 INFO @ Wed, 08 Dec 2021 18:40:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:40:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:40:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.05_summits.bed INFO @ Wed, 08 Dec 2021 18:40:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (361 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:40:34: 21000000 INFO @ Wed, 08 Dec 2021 18:40:35: 25000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:40:41: 22000000 INFO @ Wed, 08 Dec 2021 18:40:42: 26000000 INFO @ Wed, 08 Dec 2021 18:40:48: 23000000 INFO @ Wed, 08 Dec 2021 18:40:50: 27000000 INFO @ Wed, 08 Dec 2021 18:40:56: 24000000 INFO @ Wed, 08 Dec 2021 18:40:57: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:40:57: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:40:57: #1 total tags in treatment: 13847430 INFO @ Wed, 08 Dec 2021 18:40:57: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:40:57: #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 18:40:57: #1 tags after filtering in treatment: 12925039 INFO @ Wed, 08 Dec 2021 18:40:57: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:40:57: #1 finished! INFO @ Wed, 08 Dec 2021 18:40:57: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:40:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:40:58: #2 number of paired peaks: 304 WARNING @ Wed, 08 Dec 2021 18:40:58: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Wed, 08 Dec 2021 18:40:58: start model_add_line... INFO @ Wed, 08 Dec 2021 18:40:58: start X-correlation... INFO @ Wed, 08 Dec 2021 18:40:58: end of X-cor INFO @ Wed, 08 Dec 2021 18:40:58: #2 finished! INFO @ Wed, 08 Dec 2021 18:40:58: #2 predicted fragment length is 153 bps INFO @ Wed, 08 Dec 2021 18:40:58: #2 alternative fragment length(s) may be 4,153 bps INFO @ Wed, 08 Dec 2021 18:40:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.10_model.r INFO @ Wed, 08 Dec 2021 18:40:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:40:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:41:02: 25000000 INFO @ Wed, 08 Dec 2021 18:41:08: 26000000 INFO @ Wed, 08 Dec 2021 18:41:15: 27000000 INFO @ Wed, 08 Dec 2021 18:41:21: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:41:21: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:41:21: #1 total tags in treatment: 13847430 INFO @ Wed, 08 Dec 2021 18:41:21: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:41:21: #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 18:41:21: #1 tags after filtering in treatment: 12925039 INFO @ Wed, 08 Dec 2021 18:41:21: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 18:41:21: #1 finished! INFO @ Wed, 08 Dec 2021 18:41:21: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:41:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:41:22: #2 number of paired peaks: 304 WARNING @ Wed, 08 Dec 2021 18:41:22: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Wed, 08 Dec 2021 18:41:22: start model_add_line... INFO @ Wed, 08 Dec 2021 18:41:22: start X-correlation... INFO @ Wed, 08 Dec 2021 18:41:22: end of X-cor INFO @ Wed, 08 Dec 2021 18:41:22: #2 finished! INFO @ Wed, 08 Dec 2021 18:41:22: #2 predicted fragment length is 153 bps INFO @ Wed, 08 Dec 2021 18:41:22: #2 alternative fragment length(s) may be 4,153 bps INFO @ Wed, 08 Dec 2021 18:41:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.20_model.r INFO @ Wed, 08 Dec 2021 18:41:22: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:41:22: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:41:23: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:41:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:41:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:41:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.10_summits.bed INFO @ Wed, 08 Dec 2021 18:41:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (266 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:41:46: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:41:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:41:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:41:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976714/SRX8976714.20_summits.bed INFO @ Wed, 08 Dec 2021 18:41:57: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (183 records, 4 fields): 1 millis CompletedMACS2peakCalling