Job ID = 14157928 SRX = SRX10342600 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 9744587 spots for SRR13964656/SRR13964656.sra Written 9744587 spots for SRR13964656/SRR13964656.sra Read 10665107 spots for SRR13964657/SRR13964657.sra Written 10665107 spots for SRR13964657/SRR13964657.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158169 ("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: 00:13:36 20409694 reads; of these: 20409694 (100.00%) were paired; of these: 8335315 (40.84%) aligned concordantly 0 times 10429163 (51.10%) aligned concordantly exactly 1 time 1645216 (8.06%) aligned concordantly >1 times ---- 8335315 pairs aligned concordantly 0 times; of these: 5295343 (63.53%) aligned discordantly 1 time ---- 3039972 pairs aligned 0 times concordantly or discordantly; of these: 6079944 mates make up the pairs; of these: 4098091 (67.40%) aligned 0 times 792366 (13.03%) aligned exactly 1 time 1189487 (19.56%) aligned >1 times 89.96% overall alignment rate Time searching: 00:13:36 Overall time: 00:13:36 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] 4479151 / 17362901 = 0.2580 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 13:12:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.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 13:12:30: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:12:30: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:12:35: 1000000 INFO @ Wed, 08 Dec 2021 13:12:40: 2000000 INFO @ Wed, 08 Dec 2021 13:12:45: 3000000 INFO @ Wed, 08 Dec 2021 13:12:50: 4000000 INFO @ Wed, 08 Dec 2021 13:12:55: 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 13:12:59: 6000000 INFO @ Wed, 08 Dec 2021 13:12:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.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 13:12:59: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:12:59: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:13:04: 7000000 INFO @ Wed, 08 Dec 2021 13:13:04: 1000000 INFO @ Wed, 08 Dec 2021 13:13:09: 2000000 INFO @ Wed, 08 Dec 2021 13:13:09: 8000000 INFO @ Wed, 08 Dec 2021 13:13:14: 3000000 INFO @ Wed, 08 Dec 2021 13:13:14: 9000000 INFO @ Wed, 08 Dec 2021 13:13:19: 4000000 INFO @ Wed, 08 Dec 2021 13:13:19: 10000000 INFO @ Wed, 08 Dec 2021 13:13:24: 5000000 INFO @ Wed, 08 Dec 2021 13:13:25: 11000000 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 13:13:29: 6000000 INFO @ Wed, 08 Dec 2021 13:13:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.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 13:13:29: #1 read tag files... INFO @ Wed, 08 Dec 2021 13:13:29: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 13:13:30: 12000000 INFO @ Wed, 08 Dec 2021 13:13:34: 7000000 INFO @ Wed, 08 Dec 2021 13:13:35: 13000000 INFO @ Wed, 08 Dec 2021 13:13:35: 1000000 INFO @ Wed, 08 Dec 2021 13:13:39: 8000000 INFO @ Wed, 08 Dec 2021 13:13:40: 14000000 INFO @ Wed, 08 Dec 2021 13:13:40: 2000000 INFO @ Wed, 08 Dec 2021 13:13:43: 9000000 INFO @ Wed, 08 Dec 2021 13:13:45: 15000000 INFO @ Wed, 08 Dec 2021 13:13:45: 3000000 INFO @ Wed, 08 Dec 2021 13:13:48: 10000000 INFO @ Wed, 08 Dec 2021 13:13:50: 16000000 INFO @ Wed, 08 Dec 2021 13:13:51: 4000000 INFO @ Wed, 08 Dec 2021 13:13:53: 11000000 INFO @ Wed, 08 Dec 2021 13:13:55: 17000000 INFO @ Wed, 08 Dec 2021 13:13:56: 5000000 INFO @ Wed, 08 Dec 2021 13:13:57: 12000000 INFO @ Wed, 08 Dec 2021 13:14:00: 18000000 INFO @ Wed, 08 Dec 2021 13:14:01: 6000000 INFO @ Wed, 08 Dec 2021 13:14:02: 13000000 INFO @ Wed, 08 Dec 2021 13:14:05: 19000000 INFO @ Wed, 08 Dec 2021 13:14:05: 7000000 INFO @ Wed, 08 Dec 2021 13:14:07: 14000000 INFO @ Wed, 08 Dec 2021 13:14:10: 20000000 INFO @ Wed, 08 Dec 2021 13:14:11: 8000000 INFO @ Wed, 08 Dec 2021 13:14:12: 15000000 INFO @ Wed, 08 Dec 2021 13:14:15: 21000000 INFO @ Wed, 08 Dec 2021 13:14:16: 9000000 INFO @ Wed, 08 Dec 2021 13:14:16: 16000000 INFO @ Wed, 08 Dec 2021 13:14:20: 22000000 INFO @ Wed, 08 Dec 2021 13:14:21: 10000000 INFO @ Wed, 08 Dec 2021 13:14:21: 17000000 INFO @ Wed, 08 Dec 2021 13:14:25: 23000000 INFO @ Wed, 08 Dec 2021 13:14:26: 18000000 INFO @ Wed, 08 Dec 2021 13:14:26: 11000000 INFO @ Wed, 08 Dec 2021 13:14:30: 24000000 INFO @ Wed, 08 Dec 2021 13:14:30: 19000000 INFO @ Wed, 08 Dec 2021 13:14:31: 12000000 INFO @ Wed, 08 Dec 2021 13:14:35: 25000000 INFO @ Wed, 08 Dec 2021 13:14:35: 20000000 INFO @ Wed, 08 Dec 2021 13:14:36: 13000000 INFO @ Wed, 08 Dec 2021 13:14:39: 26000000 INFO @ Wed, 08 Dec 2021 13:14:40: 21000000 INFO @ Wed, 08 Dec 2021 13:14:41: 14000000 INFO @ Wed, 08 Dec 2021 13:14:44: 22000000 INFO @ Wed, 08 Dec 2021 13:14:44: 27000000 INFO @ Wed, 08 Dec 2021 13:14:46: 15000000 INFO @ Wed, 08 Dec 2021 13:14:48: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 13:14:48: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 13:14:48: #1 total tags in treatment: 8697648 INFO @ Wed, 08 Dec 2021 13:14:48: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:14:48: #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 13:14:48: #1 tags after filtering in treatment: 8082480 INFO @ Wed, 08 Dec 2021 13:14:48: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 13:14:48: #1 finished! INFO @ Wed, 08 Dec 2021 13:14:48: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:14:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:14:49: #2 number of paired peaks: 542 WARNING @ Wed, 08 Dec 2021 13:14:49: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Wed, 08 Dec 2021 13:14:49: start model_add_line... INFO @ Wed, 08 Dec 2021 13:14:49: start X-correlation... INFO @ Wed, 08 Dec 2021 13:14:49: end of X-cor INFO @ Wed, 08 Dec 2021 13:14:49: #2 finished! INFO @ Wed, 08 Dec 2021 13:14:49: #2 predicted fragment length is 142 bps INFO @ Wed, 08 Dec 2021 13:14:49: #2 alternative fragment length(s) may be 4,142 bps INFO @ Wed, 08 Dec 2021 13:14:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.05_model.r INFO @ Wed, 08 Dec 2021 13:14:49: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:14:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:14:49: 23000000 INFO @ Wed, 08 Dec 2021 13:14:51: 16000000 INFO @ Wed, 08 Dec 2021 13:14:54: 24000000 INFO @ Wed, 08 Dec 2021 13:14:56: 17000000 INFO @ Wed, 08 Dec 2021 13:14:58: 25000000 INFO @ Wed, 08 Dec 2021 13:15:01: 18000000 INFO @ Wed, 08 Dec 2021 13:15:03: 26000000 INFO @ Wed, 08 Dec 2021 13:15:06: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:15:06: 19000000 INFO @ Wed, 08 Dec 2021 13:15:08: 27000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 13:15:11: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 13:15:11: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 13:15:11: #1 total tags in treatment: 8697648 INFO @ Wed, 08 Dec 2021 13:15:11: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:15:11: #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 13:15:11: 20000000 INFO @ Wed, 08 Dec 2021 13:15:11: #1 tags after filtering in treatment: 8082480 INFO @ Wed, 08 Dec 2021 13:15:11: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 13:15:11: #1 finished! INFO @ Wed, 08 Dec 2021 13:15:11: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:15:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:15:12: #2 number of paired peaks: 542 WARNING @ Wed, 08 Dec 2021 13:15:12: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Wed, 08 Dec 2021 13:15:12: start model_add_line... INFO @ Wed, 08 Dec 2021 13:15:12: start X-correlation... INFO @ Wed, 08 Dec 2021 13:15:12: end of X-cor INFO @ Wed, 08 Dec 2021 13:15:12: #2 finished! INFO @ Wed, 08 Dec 2021 13:15:12: #2 predicted fragment length is 142 bps INFO @ Wed, 08 Dec 2021 13:15:12: #2 alternative fragment length(s) may be 4,142 bps INFO @ Wed, 08 Dec 2021 13:15:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.10_model.r INFO @ Wed, 08 Dec 2021 13:15:12: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:15:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 13:15:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.05_peaks.xls INFO @ Wed, 08 Dec 2021 13:15:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:15:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.05_summits.bed INFO @ Wed, 08 Dec 2021 13:15:14: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (1251 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:15:16: 21000000 INFO @ Wed, 08 Dec 2021 13:15:21: 22000000 INFO @ Wed, 08 Dec 2021 13:15:26: 23000000 INFO @ Wed, 08 Dec 2021 13:15:30: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:15:31: 24000000 INFO @ Wed, 08 Dec 2021 13:15:35: 25000000 INFO @ Wed, 08 Dec 2021 13:15:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.10_peaks.xls INFO @ Wed, 08 Dec 2021 13:15:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:15:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.10_summits.bed INFO @ Wed, 08 Dec 2021 13:15:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (425 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 13:15:40: 26000000 INFO @ Wed, 08 Dec 2021 13:15:45: 27000000 INFO @ Wed, 08 Dec 2021 13:15:49: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 13:15:49: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 13:15:49: #1 total tags in treatment: 8697648 INFO @ Wed, 08 Dec 2021 13:15:49: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 13:15:49: #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 13:15:49: #1 tags after filtering in treatment: 8082480 INFO @ Wed, 08 Dec 2021 13:15:49: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 13:15:49: #1 finished! INFO @ Wed, 08 Dec 2021 13:15:49: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 13:15:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 13:15:49: #2 number of paired peaks: 542 WARNING @ Wed, 08 Dec 2021 13:15:49: Fewer paired peaks (542) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 542 pairs to build model! INFO @ Wed, 08 Dec 2021 13:15:49: start model_add_line... INFO @ Wed, 08 Dec 2021 13:15:49: start X-correlation... INFO @ Wed, 08 Dec 2021 13:15:49: end of X-cor INFO @ Wed, 08 Dec 2021 13:15:49: #2 finished! INFO @ Wed, 08 Dec 2021 13:15:49: #2 predicted fragment length is 142 bps INFO @ Wed, 08 Dec 2021 13:15:49: #2 alternative fragment length(s) may be 4,142 bps INFO @ Wed, 08 Dec 2021 13:15:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.20_model.r INFO @ Wed, 08 Dec 2021 13:15:49: #3 Call peaks... INFO @ Wed, 08 Dec 2021 13:15:49: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 13:16:06: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 13:16:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.20_peaks.xls INFO @ Wed, 08 Dec 2021 13:16:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 13:16:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342600/SRX10342600.20_summits.bed INFO @ Wed, 08 Dec 2021 13:16:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (211 records, 4 fields): 2 millis CompletedMACS2peakCalling