Job ID = 14159088 SRX = SRX8976735 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 12863177 spots for SRR12483279/SRR12483279.sra Written 12863177 spots for SRR12483279/SRR12483279.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159336 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:09:52 12863177 reads; of these: 12863177 (100.00%) were paired; of these: 1176172 (9.14%) aligned concordantly 0 times 10153501 (78.93%) aligned concordantly exactly 1 time 1533504 (11.92%) aligned concordantly >1 times ---- 1176172 pairs aligned concordantly 0 times; of these: 888689 (75.56%) aligned discordantly 1 time ---- 287483 pairs aligned 0 times concordantly or discordantly; of these: 574966 mates make up the pairs; of these: 148323 (25.80%) aligned 0 times 183479 (31.91%) aligned exactly 1 time 243164 (42.29%) aligned >1 times 99.42% overall alignment rate Time searching: 00:09:53 Overall time: 00:09:53 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 8 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] 360845 / 12549015 = 0.0288 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 19:24:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.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 19:24:30: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:24:30: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:24:34: 1000000 INFO @ Wed, 08 Dec 2021 19:24:38: 2000000 INFO @ Wed, 08 Dec 2021 19:24:42: 3000000 INFO @ Wed, 08 Dec 2021 19:24:46: 4000000 INFO @ Wed, 08 Dec 2021 19:24:50: 5000000 INFO @ Wed, 08 Dec 2021 19:24:54: 6000000 INFO @ Wed, 08 Dec 2021 19:24:58: 7000000 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 19:25:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.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 19:25:00: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:25:00: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:25:01: 8000000 INFO @ Wed, 08 Dec 2021 19:25:05: 1000000 INFO @ Wed, 08 Dec 2021 19:25:05: 9000000 INFO @ Wed, 08 Dec 2021 19:25:09: 10000000 INFO @ Wed, 08 Dec 2021 19:25:09: 2000000 INFO @ Wed, 08 Dec 2021 19:25:13: 11000000 INFO @ Wed, 08 Dec 2021 19:25:14: 3000000 INFO @ Wed, 08 Dec 2021 19:25:17: 12000000 INFO @ Wed, 08 Dec 2021 19:25:19: 4000000 INFO @ Wed, 08 Dec 2021 19:25:21: 13000000 INFO @ Wed, 08 Dec 2021 19:25:23: 5000000 INFO @ Wed, 08 Dec 2021 19:25:25: 14000000 INFO @ Wed, 08 Dec 2021 19:25:28: 6000000 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 19:25:29: 15000000 INFO @ Wed, 08 Dec 2021 19:25:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.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 19:25:31: #1 read tag files... INFO @ Wed, 08 Dec 2021 19:25:31: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 19:25:32: 7000000 INFO @ Wed, 08 Dec 2021 19:25:33: 16000000 INFO @ Wed, 08 Dec 2021 19:25:35: 1000000 INFO @ Wed, 08 Dec 2021 19:25:37: 8000000 INFO @ Wed, 08 Dec 2021 19:25:37: 17000000 INFO @ Wed, 08 Dec 2021 19:25:39: 2000000 INFO @ Wed, 08 Dec 2021 19:25:41: 9000000 INFO @ Wed, 08 Dec 2021 19:25:41: 18000000 INFO @ Wed, 08 Dec 2021 19:25:43: 3000000 INFO @ Wed, 08 Dec 2021 19:25:46: 19000000 INFO @ Wed, 08 Dec 2021 19:25:46: 10000000 INFO @ Wed, 08 Dec 2021 19:25:47: 4000000 INFO @ Wed, 08 Dec 2021 19:25:50: 20000000 INFO @ Wed, 08 Dec 2021 19:25:50: 11000000 INFO @ Wed, 08 Dec 2021 19:25:51: 5000000 INFO @ Wed, 08 Dec 2021 19:25:54: 21000000 INFO @ Wed, 08 Dec 2021 19:25:55: 12000000 INFO @ Wed, 08 Dec 2021 19:25:56: 6000000 INFO @ Wed, 08 Dec 2021 19:25:57: 22000000 INFO @ Wed, 08 Dec 2021 19:26:00: 7000000 INFO @ Wed, 08 Dec 2021 19:26:00: 13000000 INFO @ Wed, 08 Dec 2021 19:26:02: 23000000 INFO @ Wed, 08 Dec 2021 19:26:04: 8000000 INFO @ Wed, 08 Dec 2021 19:26:04: 14000000 INFO @ Wed, 08 Dec 2021 19:26:06: 24000000 INFO @ Wed, 08 Dec 2021 19:26:08: 9000000 INFO @ Wed, 08 Dec 2021 19:26:09: 15000000 INFO @ Wed, 08 Dec 2021 19:26:09: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:26:09: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:26:09: #1 total tags in treatment: 11345417 INFO @ Wed, 08 Dec 2021 19:26:09: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:26:09: #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 19:26:09: #1 tags after filtering in treatment: 10633887 INFO @ Wed, 08 Dec 2021 19:26:09: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 19:26:09: #1 finished! INFO @ Wed, 08 Dec 2021 19:26:09: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:26:09: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:26:10: #2 number of paired peaks: 356 WARNING @ Wed, 08 Dec 2021 19:26:10: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Wed, 08 Dec 2021 19:26:10: start model_add_line... INFO @ Wed, 08 Dec 2021 19:26:10: start X-correlation... INFO @ Wed, 08 Dec 2021 19:26:10: end of X-cor INFO @ Wed, 08 Dec 2021 19:26:10: #2 finished! INFO @ Wed, 08 Dec 2021 19:26:10: #2 predicted fragment length is 177 bps INFO @ Wed, 08 Dec 2021 19:26:10: #2 alternative fragment length(s) may be 4,177 bps INFO @ Wed, 08 Dec 2021 19:26:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.05_model.r INFO @ Wed, 08 Dec 2021 19:26:10: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:26:10: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:26:11: 10000000 INFO @ Wed, 08 Dec 2021 19:26:13: 16000000 INFO @ Wed, 08 Dec 2021 19:26:15: 11000000 INFO @ Wed, 08 Dec 2021 19:26:18: 17000000 INFO @ Wed, 08 Dec 2021 19:26:19: 12000000 INFO @ Wed, 08 Dec 2021 19:26:22: 18000000 INFO @ Wed, 08 Dec 2021 19:26:23: 13000000 INFO @ Wed, 08 Dec 2021 19:26:27: 19000000 INFO @ Wed, 08 Dec 2021 19:26:27: 14000000 INFO @ Wed, 08 Dec 2021 19:26:31: 15000000 INFO @ Wed, 08 Dec 2021 19:26:31: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:26:32: 20000000 INFO @ Wed, 08 Dec 2021 19:26:35: 16000000 INFO @ Wed, 08 Dec 2021 19:26:36: 21000000 INFO @ Wed, 08 Dec 2021 19:26:39: 17000000 INFO @ Wed, 08 Dec 2021 19:26:40: 22000000 INFO @ Wed, 08 Dec 2021 19:26:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.05_peaks.xls INFO @ Wed, 08 Dec 2021 19:26:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:26:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.05_summits.bed INFO @ Wed, 08 Dec 2021 19:26:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (303 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:26:43: 18000000 INFO @ Wed, 08 Dec 2021 19:26:45: 23000000 INFO @ Wed, 08 Dec 2021 19:26:47: 19000000 INFO @ Wed, 08 Dec 2021 19:26:50: 24000000 INFO @ Wed, 08 Dec 2021 19:26:51: 20000000 INFO @ Wed, 08 Dec 2021 19:26:54: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:26:54: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:26:54: #1 total tags in treatment: 11345417 INFO @ Wed, 08 Dec 2021 19:26:54: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:26:54: #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 19:26:54: #1 tags after filtering in treatment: 10633887 INFO @ Wed, 08 Dec 2021 19:26:54: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 19:26:54: #1 finished! INFO @ Wed, 08 Dec 2021 19:26:54: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:26:54: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:26:55: #2 number of paired peaks: 356 WARNING @ Wed, 08 Dec 2021 19:26:55: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Wed, 08 Dec 2021 19:26:55: start model_add_line... INFO @ Wed, 08 Dec 2021 19:26:55: start X-correlation... INFO @ Wed, 08 Dec 2021 19:26:55: end of X-cor INFO @ Wed, 08 Dec 2021 19:26:55: #2 finished! INFO @ Wed, 08 Dec 2021 19:26:55: #2 predicted fragment length is 177 bps INFO @ Wed, 08 Dec 2021 19:26:55: #2 alternative fragment length(s) may be 4,177 bps INFO @ Wed, 08 Dec 2021 19:26:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.10_model.r INFO @ Wed, 08 Dec 2021 19:26:55: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:26:55: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:26:55: 21000000 INFO @ Wed, 08 Dec 2021 19:26:59: 22000000 INFO @ Wed, 08 Dec 2021 19:27:03: 23000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 19:27:07: 24000000 INFO @ Wed, 08 Dec 2021 19:27:10: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 19:27:10: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 19:27:10: #1 total tags in treatment: 11345417 INFO @ Wed, 08 Dec 2021 19:27:10: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 19:27:10: #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 19:27:10: #1 tags after filtering in treatment: 10633887 INFO @ Wed, 08 Dec 2021 19:27:10: #1 Redundant rate of treatment: 0.06 INFO @ Wed, 08 Dec 2021 19:27:10: #1 finished! INFO @ Wed, 08 Dec 2021 19:27:10: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 19:27:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 19:27:11: #2 number of paired peaks: 356 WARNING @ Wed, 08 Dec 2021 19:27:11: Fewer paired peaks (356) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 356 pairs to build model! INFO @ Wed, 08 Dec 2021 19:27:11: start model_add_line... INFO @ Wed, 08 Dec 2021 19:27:11: start X-correlation... INFO @ Wed, 08 Dec 2021 19:27:11: end of X-cor INFO @ Wed, 08 Dec 2021 19:27:11: #2 finished! INFO @ Wed, 08 Dec 2021 19:27:11: #2 predicted fragment length is 177 bps INFO @ Wed, 08 Dec 2021 19:27:11: #2 alternative fragment length(s) may be 4,177 bps INFO @ Wed, 08 Dec 2021 19:27:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.20_model.r INFO @ Wed, 08 Dec 2021 19:27:11: #3 Call peaks... INFO @ Wed, 08 Dec 2021 19:27:11: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 19:27:16: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:27:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.10_peaks.xls INFO @ Wed, 08 Dec 2021 19:27:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:27:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.10_summits.bed INFO @ Wed, 08 Dec 2021 19:27:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (234 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 19:27:33: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 19:27:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.20_peaks.xls INFO @ Wed, 08 Dec 2021 19:27:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 19:27:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976735/SRX8976735.20_summits.bed INFO @ Wed, 08 Dec 2021 19:27:43: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (163 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。