Job ID = 14159136 SRX = SRX8976747 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 15274019 spots for SRR12483291/SRR12483291.sra Written 15274019 spots for SRR12483291/SRR12483291.sra fastq に変換しました。 bowtie でマッピング中... Your job 14159405 ("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: 00:13:26 15274019 reads; of these: 15274019 (100.00%) were paired; of these: 1848547 (12.10%) aligned concordantly 0 times 10445169 (68.39%) aligned concordantly exactly 1 time 2980303 (19.51%) aligned concordantly >1 times ---- 1848547 pairs aligned concordantly 0 times; of these: 1133144 (61.30%) aligned discordantly 1 time ---- 715403 pairs aligned 0 times concordantly or discordantly; of these: 1430806 mates make up the pairs; of these: 429686 (30.03%) aligned 0 times 340949 (23.83%) aligned exactly 1 time 660171 (46.14%) aligned >1 times 98.59% overall alignment rate Time searching: 00:13:26 Overall time: 00:13:26 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] 1152879 / 14546398 = 0.0793 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 20:07:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.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 20:07:43: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:07:43: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:07:47: 1000000 INFO @ Wed, 08 Dec 2021 20:07:51: 2000000 INFO @ Wed, 08 Dec 2021 20:07:55: 3000000 INFO @ Wed, 08 Dec 2021 20:07:59: 4000000 INFO @ Wed, 08 Dec 2021 20:08:02: 5000000 INFO @ Wed, 08 Dec 2021 20:08:06: 6000000 INFO @ Wed, 08 Dec 2021 20:08:10: 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 20:08:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.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 20:08:13: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:08:13: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:08:14: 8000000 INFO @ Wed, 08 Dec 2021 20:08:17: 1000000 INFO @ Wed, 08 Dec 2021 20:08:18: 9000000 INFO @ Wed, 08 Dec 2021 20:08:22: 10000000 INFO @ Wed, 08 Dec 2021 20:08:22: 2000000 INFO @ Wed, 08 Dec 2021 20:08:26: 11000000 INFO @ Wed, 08 Dec 2021 20:08:27: 3000000 INFO @ Wed, 08 Dec 2021 20:08:30: 12000000 INFO @ Wed, 08 Dec 2021 20:08:31: 4000000 INFO @ Wed, 08 Dec 2021 20:08:34: 13000000 INFO @ Wed, 08 Dec 2021 20:08:36: 5000000 INFO @ Wed, 08 Dec 2021 20:08:38: 14000000 INFO @ Wed, 08 Dec 2021 20:08:40: 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 20:08:42: 15000000 INFO @ Wed, 08 Dec 2021 20:08:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.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 20:08:43: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:08:43: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:08:45: 7000000 INFO @ Wed, 08 Dec 2021 20:08:46: 16000000 INFO @ Wed, 08 Dec 2021 20:08:47: 1000000 INFO @ Wed, 08 Dec 2021 20:08:50: 17000000 INFO @ Wed, 08 Dec 2021 20:08:50: 8000000 INFO @ Wed, 08 Dec 2021 20:08:51: 2000000 INFO @ Wed, 08 Dec 2021 20:08:54: 18000000 INFO @ Wed, 08 Dec 2021 20:08:54: 9000000 INFO @ Wed, 08 Dec 2021 20:08:55: 3000000 INFO @ Wed, 08 Dec 2021 20:08:58: 19000000 INFO @ Wed, 08 Dec 2021 20:08:59: 4000000 INFO @ Wed, 08 Dec 2021 20:08:59: 10000000 INFO @ Wed, 08 Dec 2021 20:09:02: 20000000 INFO @ Wed, 08 Dec 2021 20:09:02: 5000000 INFO @ Wed, 08 Dec 2021 20:09:04: 11000000 INFO @ Wed, 08 Dec 2021 20:09:06: 21000000 INFO @ Wed, 08 Dec 2021 20:09:06: 6000000 INFO @ Wed, 08 Dec 2021 20:09:08: 12000000 INFO @ Wed, 08 Dec 2021 20:09:10: 22000000 INFO @ Wed, 08 Dec 2021 20:09:10: 7000000 INFO @ Wed, 08 Dec 2021 20:09:13: 13000000 INFO @ Wed, 08 Dec 2021 20:09:13: 23000000 INFO @ Wed, 08 Dec 2021 20:09:14: 8000000 INFO @ Wed, 08 Dec 2021 20:09:17: 24000000 INFO @ Wed, 08 Dec 2021 20:09:17: 14000000 INFO @ Wed, 08 Dec 2021 20:09:18: 9000000 INFO @ Wed, 08 Dec 2021 20:09:21: 25000000 INFO @ Wed, 08 Dec 2021 20:09:22: 15000000 INFO @ Wed, 08 Dec 2021 20:09:22: 10000000 INFO @ Wed, 08 Dec 2021 20:09:25: 26000000 INFO @ Wed, 08 Dec 2021 20:09:26: 11000000 INFO @ Wed, 08 Dec 2021 20:09:27: 16000000 INFO @ Wed, 08 Dec 2021 20:09:29: 27000000 INFO @ Wed, 08 Dec 2021 20:09:30: 12000000 INFO @ Wed, 08 Dec 2021 20:09:31: 17000000 INFO @ Wed, 08 Dec 2021 20:09:33: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 20:09:33: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 20:09:33: #1 total tags in treatment: 12337666 INFO @ Wed, 08 Dec 2021 20:09:33: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:09:33: #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 20:09:33: #1 tags after filtering in treatment: 10591348 INFO @ Wed, 08 Dec 2021 20:09:33: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 08 Dec 2021 20:09:33: #1 finished! INFO @ Wed, 08 Dec 2021 20:09:33: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:09:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:09:34: #2 number of paired peaks: 1403 INFO @ Wed, 08 Dec 2021 20:09:34: start model_add_line... INFO @ Wed, 08 Dec 2021 20:09:34: start X-correlation... INFO @ Wed, 08 Dec 2021 20:09:34: end of X-cor INFO @ Wed, 08 Dec 2021 20:09:34: #2 finished! INFO @ Wed, 08 Dec 2021 20:09:34: #2 predicted fragment length is 185 bps INFO @ Wed, 08 Dec 2021 20:09:34: #2 alternative fragment length(s) may be 2,153,164,185,199,219 bps INFO @ Wed, 08 Dec 2021 20:09:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.05_model.r INFO @ Wed, 08 Dec 2021 20:09:34: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:09:34: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:09:34: 13000000 INFO @ Wed, 08 Dec 2021 20:09:36: 18000000 INFO @ Wed, 08 Dec 2021 20:09:38: 14000000 INFO @ Wed, 08 Dec 2021 20:09:41: 19000000 INFO @ Wed, 08 Dec 2021 20:09:43: 15000000 INFO @ Wed, 08 Dec 2021 20:09:45: 20000000 INFO @ Wed, 08 Dec 2021 20:09:47: 16000000 INFO @ Wed, 08 Dec 2021 20:09:50: 21000000 INFO @ Wed, 08 Dec 2021 20:09:51: 17000000 INFO @ Wed, 08 Dec 2021 20:09:55: 18000000 INFO @ Wed, 08 Dec 2021 20:09:55: 22000000 INFO @ Wed, 08 Dec 2021 20:09:58: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:09:59: 19000000 INFO @ Wed, 08 Dec 2021 20:09:59: 23000000 INFO @ Wed, 08 Dec 2021 20:10:02: 20000000 INFO @ Wed, 08 Dec 2021 20:10:04: 24000000 INFO @ Wed, 08 Dec 2021 20:10:06: 21000000 INFO @ Wed, 08 Dec 2021 20:10:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:10:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:10:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.05_summits.bed INFO @ Wed, 08 Dec 2021 20:10:08: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (830 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:10:09: 25000000 INFO @ Wed, 08 Dec 2021 20:10:10: 22000000 INFO @ Wed, 08 Dec 2021 20:10:13: 26000000 INFO @ Wed, 08 Dec 2021 20:10:14: 23000000 INFO @ Wed, 08 Dec 2021 20:10:18: 27000000 INFO @ Wed, 08 Dec 2021 20:10:18: 24000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:10:22: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 20:10:22: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 20:10:22: #1 total tags in treatment: 12337666 INFO @ Wed, 08 Dec 2021 20:10:22: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:10:22: #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 20:10:22: #1 tags after filtering in treatment: 10591348 INFO @ Wed, 08 Dec 2021 20:10:22: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 08 Dec 2021 20:10:22: #1 finished! INFO @ Wed, 08 Dec 2021 20:10:22: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:10:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:10:22: 25000000 INFO @ Wed, 08 Dec 2021 20:10:23: #2 number of paired peaks: 1403 INFO @ Wed, 08 Dec 2021 20:10:23: start model_add_line... INFO @ Wed, 08 Dec 2021 20:10:23: start X-correlation... INFO @ Wed, 08 Dec 2021 20:10:23: end of X-cor INFO @ Wed, 08 Dec 2021 20:10:23: #2 finished! INFO @ Wed, 08 Dec 2021 20:10:23: #2 predicted fragment length is 185 bps INFO @ Wed, 08 Dec 2021 20:10:23: #2 alternative fragment length(s) may be 2,153,164,185,199,219 bps INFO @ Wed, 08 Dec 2021 20:10:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.10_model.r INFO @ Wed, 08 Dec 2021 20:10:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:10:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:10:26: 26000000 INFO @ Wed, 08 Dec 2021 20:10:30: 27000000 INFO @ Wed, 08 Dec 2021 20:10:34: #1 tag size is determined as 42 bps INFO @ Wed, 08 Dec 2021 20:10:34: #1 tag size = 42 INFO @ Wed, 08 Dec 2021 20:10:34: #1 total tags in treatment: 12337666 INFO @ Wed, 08 Dec 2021 20:10:34: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:10:34: #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 20:10:34: #1 tags after filtering in treatment: 10591348 INFO @ Wed, 08 Dec 2021 20:10:34: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 08 Dec 2021 20:10:34: #1 finished! INFO @ Wed, 08 Dec 2021 20:10:34: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:10:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:10:35: #2 number of paired peaks: 1403 INFO @ Wed, 08 Dec 2021 20:10:35: start model_add_line... INFO @ Wed, 08 Dec 2021 20:10:35: start X-correlation... INFO @ Wed, 08 Dec 2021 20:10:35: end of X-cor INFO @ Wed, 08 Dec 2021 20:10:35: #2 finished! INFO @ Wed, 08 Dec 2021 20:10:35: #2 predicted fragment length is 185 bps INFO @ Wed, 08 Dec 2021 20:10:35: #2 alternative fragment length(s) may be 2,153,164,185,199,219 bps INFO @ Wed, 08 Dec 2021 20:10:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.20_model.r INFO @ Wed, 08 Dec 2021 20:10:35: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:10:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:10:47: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:10:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:10:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:10:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.10_summits.bed INFO @ Wed, 08 Dec 2021 20:10:57: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (373 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:10:59: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:11:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:11:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:11:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX8976747/SRX8976747.20_summits.bed INFO @ Wed, 08 Dec 2021 20:11:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (200 records, 4 fields): 1 millis CompletedMACS2peakCalling