Job ID = 14158164 SRX = SRX10342577 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 20067352 spots for SRR13964610/SRR13964610.sra Written 20067352 spots for SRR13964610/SRR13964610.sra Read 20136865 spots for SRR13964611/SRR13964611.sra Written 20136865 spots for SRR13964611/SRR13964611.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158724 ("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: 00:42:51 40204217 reads; of these: 40204217 (100.00%) were paired; of these: 7709590 (19.18%) aligned concordantly 0 times 23926756 (59.51%) aligned concordantly exactly 1 time 8567871 (21.31%) aligned concordantly >1 times ---- 7709590 pairs aligned concordantly 0 times; of these: 1408136 (18.26%) aligned discordantly 1 time ---- 6301454 pairs aligned 0 times concordantly or discordantly; of these: 12602908 mates make up the pairs; of these: 10867421 (86.23%) aligned 0 times 785074 (6.23%) aligned exactly 1 time 950413 (7.54%) aligned >1 times 86.48% overall alignment rate Time searching: 00:42:51 Overall time: 00:42:51 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 32 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] 18255832 / 33813935 = 0.5399 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 15:32:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.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 15:32:39: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:32:39: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:32:44: 1000000 INFO @ Wed, 08 Dec 2021 15:32:49: 2000000 INFO @ Wed, 08 Dec 2021 15:32:54: 3000000 INFO @ Wed, 08 Dec 2021 15:33:00: 4000000 INFO @ Wed, 08 Dec 2021 15:33:05: 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 15:33:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.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 15:33:09: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:33:09: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:33:10: 6000000 INFO @ Wed, 08 Dec 2021 15:33:14: 1000000 INFO @ Wed, 08 Dec 2021 15:33:16: 7000000 INFO @ Wed, 08 Dec 2021 15:33:19: 2000000 INFO @ Wed, 08 Dec 2021 15:33:22: 8000000 INFO @ Wed, 08 Dec 2021 15:33:23: 3000000 INFO @ Wed, 08 Dec 2021 15:33:27: 9000000 INFO @ Wed, 08 Dec 2021 15:33:28: 4000000 INFO @ Wed, 08 Dec 2021 15:33:33: 10000000 INFO @ Wed, 08 Dec 2021 15:33:33: 5000000 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 15:33:38: 11000000 INFO @ Wed, 08 Dec 2021 15:33:38: 6000000 INFO @ Wed, 08 Dec 2021 15:33:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.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 15:33:39: #1 read tag files... INFO @ Wed, 08 Dec 2021 15:33:39: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 15:33:43: 12000000 INFO @ Wed, 08 Dec 2021 15:33:43: 7000000 INFO @ Wed, 08 Dec 2021 15:33:44: 1000000 INFO @ Wed, 08 Dec 2021 15:33:48: 8000000 INFO @ Wed, 08 Dec 2021 15:33:48: 13000000 INFO @ Wed, 08 Dec 2021 15:33:49: 2000000 INFO @ Wed, 08 Dec 2021 15:33:53: 9000000 INFO @ Wed, 08 Dec 2021 15:33:54: 3000000 INFO @ Wed, 08 Dec 2021 15:33:54: 14000000 INFO @ Wed, 08 Dec 2021 15:33:58: 10000000 INFO @ Wed, 08 Dec 2021 15:33:59: 4000000 INFO @ Wed, 08 Dec 2021 15:34:00: 15000000 INFO @ Wed, 08 Dec 2021 15:34:04: 11000000 INFO @ Wed, 08 Dec 2021 15:34:05: 5000000 INFO @ Wed, 08 Dec 2021 15:34:05: 16000000 INFO @ Wed, 08 Dec 2021 15:34:09: 12000000 INFO @ Wed, 08 Dec 2021 15:34:10: 6000000 INFO @ Wed, 08 Dec 2021 15:34:10: 17000000 INFO @ Wed, 08 Dec 2021 15:34:14: 13000000 INFO @ Wed, 08 Dec 2021 15:34:15: 7000000 INFO @ Wed, 08 Dec 2021 15:34:16: 18000000 INFO @ Wed, 08 Dec 2021 15:34:20: 14000000 INFO @ Wed, 08 Dec 2021 15:34:21: 8000000 INFO @ Wed, 08 Dec 2021 15:34:21: 19000000 INFO @ Wed, 08 Dec 2021 15:34:25: 15000000 INFO @ Wed, 08 Dec 2021 15:34:26: 9000000 INFO @ Wed, 08 Dec 2021 15:34:27: 20000000 INFO @ Wed, 08 Dec 2021 15:34:30: 16000000 INFO @ Wed, 08 Dec 2021 15:34:31: 10000000 INFO @ Wed, 08 Dec 2021 15:34:32: 21000000 INFO @ Wed, 08 Dec 2021 15:34:36: 17000000 INFO @ Wed, 08 Dec 2021 15:34:37: 11000000 INFO @ Wed, 08 Dec 2021 15:34:38: 22000000 INFO @ Wed, 08 Dec 2021 15:34:41: 18000000 INFO @ Wed, 08 Dec 2021 15:34:42: 12000000 INFO @ Wed, 08 Dec 2021 15:34:43: 23000000 INFO @ Wed, 08 Dec 2021 15:34:46: 19000000 INFO @ Wed, 08 Dec 2021 15:34:47: 13000000 INFO @ Wed, 08 Dec 2021 15:34:48: 24000000 INFO @ Wed, 08 Dec 2021 15:34:52: 20000000 INFO @ Wed, 08 Dec 2021 15:34:53: 14000000 INFO @ Wed, 08 Dec 2021 15:34:54: 25000000 INFO @ Wed, 08 Dec 2021 15:34:57: 21000000 INFO @ Wed, 08 Dec 2021 15:34:58: 15000000 INFO @ Wed, 08 Dec 2021 15:34:59: 26000000 INFO @ Wed, 08 Dec 2021 15:35:02: 22000000 INFO @ Wed, 08 Dec 2021 15:35:03: 16000000 INFO @ Wed, 08 Dec 2021 15:35:04: 27000000 INFO @ Wed, 08 Dec 2021 15:35:08: 23000000 INFO @ Wed, 08 Dec 2021 15:35:09: 17000000 INFO @ Wed, 08 Dec 2021 15:35:10: 28000000 INFO @ Wed, 08 Dec 2021 15:35:13: 24000000 INFO @ Wed, 08 Dec 2021 15:35:14: 18000000 INFO @ Wed, 08 Dec 2021 15:35:15: 29000000 INFO @ Wed, 08 Dec 2021 15:35:18: 25000000 INFO @ Wed, 08 Dec 2021 15:35:19: 19000000 INFO @ Wed, 08 Dec 2021 15:35:20: 30000000 INFO @ Wed, 08 Dec 2021 15:35:23: 26000000 INFO @ Wed, 08 Dec 2021 15:35:24: 20000000 INFO @ Wed, 08 Dec 2021 15:35:25: 31000000 INFO @ Wed, 08 Dec 2021 15:35:28: 27000000 INFO @ Wed, 08 Dec 2021 15:35:30: 21000000 INFO @ Wed, 08 Dec 2021 15:35:31: 32000000 INFO @ Wed, 08 Dec 2021 15:35:33: 28000000 INFO @ Wed, 08 Dec 2021 15:35:35: 22000000 INFO @ Wed, 08 Dec 2021 15:35:36: 33000000 INFO @ Wed, 08 Dec 2021 15:35:36: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 15:35:36: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 15:35:36: #1 total tags in treatment: 14804584 INFO @ Wed, 08 Dec 2021 15:35:36: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:35:36: #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 15:35:36: #1 tags after filtering in treatment: 11324094 INFO @ Wed, 08 Dec 2021 15:35:36: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 08 Dec 2021 15:35:36: #1 finished! INFO @ Wed, 08 Dec 2021 15:35:36: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:35:36: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 15:35:37: #2 number of paired peaks: 942 WARNING @ Wed, 08 Dec 2021 15:35:37: Fewer paired peaks (942) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 942 pairs to build model! INFO @ Wed, 08 Dec 2021 15:35:37: start model_add_line... INFO @ Wed, 08 Dec 2021 15:35:37: start X-correlation... INFO @ Wed, 08 Dec 2021 15:35:37: end of X-cor INFO @ Wed, 08 Dec 2021 15:35:37: #2 finished! INFO @ Wed, 08 Dec 2021 15:35:37: #2 predicted fragment length is 147 bps INFO @ Wed, 08 Dec 2021 15:35:37: #2 alternative fragment length(s) may be 4,147 bps INFO @ Wed, 08 Dec 2021 15:35:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.05_model.r INFO @ Wed, 08 Dec 2021 15:35:37: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:35:37: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:35:38: 29000000 INFO @ Wed, 08 Dec 2021 15:35:40: 23000000 INFO @ Wed, 08 Dec 2021 15:35:43: 30000000 INFO @ Wed, 08 Dec 2021 15:35:44: 24000000 INFO @ Wed, 08 Dec 2021 15:35:48: 31000000 INFO @ Wed, 08 Dec 2021 15:35:49: 25000000 INFO @ Wed, 08 Dec 2021 15:35:52: 32000000 INFO @ Wed, 08 Dec 2021 15:35:54: 26000000 INFO @ Wed, 08 Dec 2021 15:35:57: 33000000 INFO @ Wed, 08 Dec 2021 15:35:57: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 15:35:57: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 15:35:57: #1 total tags in treatment: 14804584 INFO @ Wed, 08 Dec 2021 15:35:57: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:35:57: #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 15:35:57: #1 tags after filtering in treatment: 11324094 INFO @ Wed, 08 Dec 2021 15:35:57: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 08 Dec 2021 15:35:57: #1 finished! INFO @ Wed, 08 Dec 2021 15:35:57: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:35:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:35:58: 27000000 INFO @ Wed, 08 Dec 2021 15:35:58: #2 number of paired peaks: 942 WARNING @ Wed, 08 Dec 2021 15:35:58: Fewer paired peaks (942) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 942 pairs to build model! INFO @ Wed, 08 Dec 2021 15:35:58: start model_add_line... INFO @ Wed, 08 Dec 2021 15:35:58: start X-correlation... INFO @ Wed, 08 Dec 2021 15:35:58: end of X-cor INFO @ Wed, 08 Dec 2021 15:35:58: #2 finished! INFO @ Wed, 08 Dec 2021 15:35:58: #2 predicted fragment length is 147 bps INFO @ Wed, 08 Dec 2021 15:35:58: #2 alternative fragment length(s) may be 4,147 bps INFO @ Wed, 08 Dec 2021 15:35:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.10_model.r INFO @ Wed, 08 Dec 2021 15:35:58: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:35:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 15:36:01: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:36:03: 28000000 INFO @ Wed, 08 Dec 2021 15:36:07: 29000000 INFO @ Wed, 08 Dec 2021 15:36:11: 30000000 INFO @ Wed, 08 Dec 2021 15:36:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.05_peaks.xls INFO @ Wed, 08 Dec 2021 15:36:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:36:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.05_summits.bed INFO @ Wed, 08 Dec 2021 15:36:12: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1991 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:36:16: 31000000 INFO @ Wed, 08 Dec 2021 15:36:20: 32000000 INFO @ Wed, 08 Dec 2021 15:36:22: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:36:25: 33000000 INFO @ Wed, 08 Dec 2021 15:36:25: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 15:36:25: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 15:36:25: #1 total tags in treatment: 14804584 INFO @ Wed, 08 Dec 2021 15:36:25: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 15:36:25: #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 15:36:25: #1 tags after filtering in treatment: 11324094 INFO @ Wed, 08 Dec 2021 15:36:25: #1 Redundant rate of treatment: 0.24 INFO @ Wed, 08 Dec 2021 15:36:25: #1 finished! INFO @ Wed, 08 Dec 2021 15:36:25: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 15:36:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 15:36:26: #2 number of paired peaks: 942 WARNING @ Wed, 08 Dec 2021 15:36:26: Fewer paired peaks (942) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 942 pairs to build model! INFO @ Wed, 08 Dec 2021 15:36:26: start model_add_line... INFO @ Wed, 08 Dec 2021 15:36:26: start X-correlation... INFO @ Wed, 08 Dec 2021 15:36:26: end of X-cor INFO @ Wed, 08 Dec 2021 15:36:26: #2 finished! INFO @ Wed, 08 Dec 2021 15:36:26: #2 predicted fragment length is 147 bps INFO @ Wed, 08 Dec 2021 15:36:26: #2 alternative fragment length(s) may be 4,147 bps INFO @ Wed, 08 Dec 2021 15:36:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.20_model.r INFO @ Wed, 08 Dec 2021 15:36:26: #3 Call peaks... INFO @ Wed, 08 Dec 2021 15:36:26: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 15:36:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.10_peaks.xls INFO @ Wed, 08 Dec 2021 15:36:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:36:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.10_summits.bed INFO @ Wed, 08 Dec 2021 15:36:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1101 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 15:36:50: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 15:37:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.20_peaks.xls INFO @ Wed, 08 Dec 2021 15:37:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 15:37:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342577/SRX10342577.20_summits.bed INFO @ Wed, 08 Dec 2021 15:37:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (592 records, 4 fields): 1 millis CompletedMACS2peakCalling