Job ID = 14158722 SRX = SRX8976706 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 13112146 spots for SRR12483310/SRR12483310.sra Written 13112146 spots for SRR12483310/SRR12483310.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159167 ("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: 00:12:38 13112146 reads; of these: 13112146 (100.00%) were paired; of these: 2189276 (16.70%) aligned concordantly 0 times 8663486 (66.07%) aligned concordantly exactly 1 time 2259384 (17.23%) aligned concordantly >1 times ---- 2189276 pairs aligned concordantly 0 times; of these: 1474335 (67.34%) aligned discordantly 1 time ---- 714941 pairs aligned 0 times concordantly or discordantly; of these: 1429882 mates make up the pairs; of these: 453671 (31.73%) aligned 0 times 391003 (27.35%) aligned exactly 1 time 585208 (40.93%) aligned >1 times 98.27% overall alignment rate Time searching: 00:12:38 Overall time: 00:12:38 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] 3353274 / 12390720 = 0.2706 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 18:02:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.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 18:02:18: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:02:18: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:02:23: 1000000 INFO @ Wed, 08 Dec 2021 18:02:29: 2000000 INFO @ Wed, 08 Dec 2021 18:02:34: 3000000 INFO @ Wed, 08 Dec 2021 18:02:39: 4000000 INFO @ Wed, 08 Dec 2021 18:02:44: 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 18:02:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.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 18:02:48: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:02:48: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:02:50: 6000000 INFO @ Wed, 08 Dec 2021 18:02:55: 1000000 INFO @ Wed, 08 Dec 2021 18:02:57: 7000000 INFO @ Wed, 08 Dec 2021 18:03:03: 2000000 INFO @ Wed, 08 Dec 2021 18:03:04: 8000000 INFO @ Wed, 08 Dec 2021 18:03:10: 3000000 INFO @ Wed, 08 Dec 2021 18:03:11: 9000000 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 18:03:18: 4000000 INFO @ Wed, 08 Dec 2021 18:03:18: 10000000 INFO @ Wed, 08 Dec 2021 18:03:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.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 18:03:18: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:03:18: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:03:25: 11000000 INFO @ Wed, 08 Dec 2021 18:03:25: 1000000 INFO @ Wed, 08 Dec 2021 18:03:26: 5000000 INFO @ Wed, 08 Dec 2021 18:03:32: 12000000 INFO @ Wed, 08 Dec 2021 18:03:33: 2000000 INFO @ Wed, 08 Dec 2021 18:03:33: 6000000 INFO @ Wed, 08 Dec 2021 18:03:39: 13000000 INFO @ Wed, 08 Dec 2021 18:03:41: 3000000 INFO @ Wed, 08 Dec 2021 18:03:41: 7000000 INFO @ Wed, 08 Dec 2021 18:03:46: 14000000 INFO @ Wed, 08 Dec 2021 18:03:49: 4000000 INFO @ Wed, 08 Dec 2021 18:03:49: 8000000 INFO @ Wed, 08 Dec 2021 18:03:53: 15000000 INFO @ Wed, 08 Dec 2021 18:03:56: 5000000 INFO @ Wed, 08 Dec 2021 18:03:57: 9000000 INFO @ Wed, 08 Dec 2021 18:04:00: 16000000 INFO @ Wed, 08 Dec 2021 18:04:04: 6000000 INFO @ Wed, 08 Dec 2021 18:04:04: 10000000 INFO @ Wed, 08 Dec 2021 18:04:06: 17000000 INFO @ Wed, 08 Dec 2021 18:04:12: 7000000 INFO @ Wed, 08 Dec 2021 18:04:12: 11000000 INFO @ Wed, 08 Dec 2021 18:04:13: 18000000 INFO @ Wed, 08 Dec 2021 18:04:20: 12000000 INFO @ Wed, 08 Dec 2021 18:04:20: 8000000 INFO @ Wed, 08 Dec 2021 18:04:20: 19000000 INFO @ Wed, 08 Dec 2021 18:04:21: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:04:21: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:04:21: #1 total tags in treatment: 7867187 INFO @ Wed, 08 Dec 2021 18:04:21: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:04:21: #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 18:04:21: #1 tags after filtering in treatment: 7026871 INFO @ Wed, 08 Dec 2021 18:04:21: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 08 Dec 2021 18:04:21: #1 finished! INFO @ Wed, 08 Dec 2021 18:04:21: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:04:21: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:04:21: #2 number of paired peaks: 748 WARNING @ Wed, 08 Dec 2021 18:04:21: Fewer paired peaks (748) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 748 pairs to build model! INFO @ Wed, 08 Dec 2021 18:04:21: start model_add_line... INFO @ Wed, 08 Dec 2021 18:04:21: start X-correlation... INFO @ Wed, 08 Dec 2021 18:04:21: end of X-cor INFO @ Wed, 08 Dec 2021 18:04:21: #2 finished! INFO @ Wed, 08 Dec 2021 18:04:21: #2 predicted fragment length is 161 bps INFO @ Wed, 08 Dec 2021 18:04:21: #2 alternative fragment length(s) may be 4,161 bps INFO @ Wed, 08 Dec 2021 18:04:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.05_model.r INFO @ Wed, 08 Dec 2021 18:04:21: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:04:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:04:27: 13000000 INFO @ Wed, 08 Dec 2021 18:04:28: 9000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:04:34: 14000000 INFO @ Wed, 08 Dec 2021 18:04:35: 10000000 INFO @ Wed, 08 Dec 2021 18:04:38: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:04:42: 15000000 INFO @ Wed, 08 Dec 2021 18:04:43: 11000000 INFO @ Wed, 08 Dec 2021 18:04:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:04:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:04:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.05_summits.bed INFO @ Wed, 08 Dec 2021 18:04:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (824 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:04:49: 16000000 INFO @ Wed, 08 Dec 2021 18:04:51: 12000000 INFO @ Wed, 08 Dec 2021 18:04:56: 17000000 INFO @ Wed, 08 Dec 2021 18:04:58: 13000000 INFO @ Wed, 08 Dec 2021 18:05:03: 18000000 INFO @ Wed, 08 Dec 2021 18:05:06: 14000000 INFO @ Wed, 08 Dec 2021 18:05:10: 19000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:05:11: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:05:11: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:05:11: #1 total tags in treatment: 7867187 INFO @ Wed, 08 Dec 2021 18:05:11: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:05:11: #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 18:05:11: #1 tags after filtering in treatment: 7026871 INFO @ Wed, 08 Dec 2021 18:05:11: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 08 Dec 2021 18:05:11: #1 finished! INFO @ Wed, 08 Dec 2021 18:05:11: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:05:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:05:11: #2 number of paired peaks: 748 WARNING @ Wed, 08 Dec 2021 18:05:11: Fewer paired peaks (748) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 748 pairs to build model! INFO @ Wed, 08 Dec 2021 18:05:11: start model_add_line... INFO @ Wed, 08 Dec 2021 18:05:12: start X-correlation... INFO @ Wed, 08 Dec 2021 18:05:12: end of X-cor INFO @ Wed, 08 Dec 2021 18:05:12: #2 finished! INFO @ Wed, 08 Dec 2021 18:05:12: #2 predicted fragment length is 161 bps INFO @ Wed, 08 Dec 2021 18:05:12: #2 alternative fragment length(s) may be 4,161 bps INFO @ Wed, 08 Dec 2021 18:05:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.10_model.r INFO @ Wed, 08 Dec 2021 18:05:12: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:05:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:05:13: 15000000 INFO @ Wed, 08 Dec 2021 18:05:20: 16000000 INFO @ Wed, 08 Dec 2021 18:05:27: 17000000 INFO @ Wed, 08 Dec 2021 18:05:28: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:05:33: 18000000 INFO @ Wed, 08 Dec 2021 18:05:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:05:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:05:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.10_summits.bed INFO @ Wed, 08 Dec 2021 18:05:36: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (448 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:05:40: 19000000 INFO @ Wed, 08 Dec 2021 18:05:40: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:05:40: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:05:40: #1 total tags in treatment: 7867187 INFO @ Wed, 08 Dec 2021 18:05:40: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:05:40: #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 18:05:40: #1 tags after filtering in treatment: 7026871 INFO @ Wed, 08 Dec 2021 18:05:40: #1 Redundant rate of treatment: 0.11 INFO @ Wed, 08 Dec 2021 18:05:40: #1 finished! INFO @ Wed, 08 Dec 2021 18:05:40: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:05:40: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:05:41: #2 number of paired peaks: 748 WARNING @ Wed, 08 Dec 2021 18:05:41: Fewer paired peaks (748) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 748 pairs to build model! INFO @ Wed, 08 Dec 2021 18:05:41: start model_add_line... INFO @ Wed, 08 Dec 2021 18:05:41: start X-correlation... INFO @ Wed, 08 Dec 2021 18:05:41: end of X-cor INFO @ Wed, 08 Dec 2021 18:05:41: #2 finished! INFO @ Wed, 08 Dec 2021 18:05:41: #2 predicted fragment length is 161 bps INFO @ Wed, 08 Dec 2021 18:05:41: #2 alternative fragment length(s) may be 4,161 bps INFO @ Wed, 08 Dec 2021 18:05:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.20_model.r INFO @ Wed, 08 Dec 2021 18:05:41: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:05:41: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:05:57: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:06:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:06:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:06:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976706/SRX8976706.20_summits.bed INFO @ Wed, 08 Dec 2021 18:06:05: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (260 records, 4 fields): 1 millis CompletedMACS2peakCalling