Job ID = 14159152 SRX = SRX8976701 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:18:33 16637097 reads; of these: 16637097 (100.00%) were paired; of these: 1421321 (8.54%) aligned concordantly 0 times 13180695 (79.22%) aligned concordantly exactly 1 time 2035081 (12.23%) aligned concordantly >1 times ---- 1421321 pairs aligned concordantly 0 times; of these: 974866 (68.59%) aligned discordantly 1 time ---- 446455 pairs aligned 0 times concordantly or discordantly; of these: 892910 mates make up the pairs; of these: 356145 (39.89%) aligned 0 times 273851 (30.67%) aligned exactly 1 time 262914 (29.44%) aligned >1 times 98.93% overall alignment rate Time searching: 00:18:33 Overall time: 00:18:33 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 16 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] 284301 / 16168981 = 0.0176 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 20:22:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.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 20:22:37: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:22:37: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:22:45: 1000000 INFO @ Wed, 08 Dec 2021 20:22:53: 2000000 INFO @ Wed, 08 Dec 2021 20:23:00: 3000000 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 20:23:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.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 20:23:06: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:23:06: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:23:07: 4000000 INFO @ Wed, 08 Dec 2021 20:23:15: 5000000 INFO @ Wed, 08 Dec 2021 20:23:16: 1000000 INFO @ Wed, 08 Dec 2021 20:23:22: 6000000 INFO @ Wed, 08 Dec 2021 20:23:26: 2000000 INFO @ Wed, 08 Dec 2021 20:23:29: 7000000 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 20:23:35: 3000000 INFO @ Wed, 08 Dec 2021 20:23:36: 8000000 INFO @ Wed, 08 Dec 2021 20:23:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.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 20:23:36: #1 read tag files... INFO @ Wed, 08 Dec 2021 20:23:36: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 20:23:44: 9000000 INFO @ Wed, 08 Dec 2021 20:23:45: 4000000 INFO @ Wed, 08 Dec 2021 20:23:47: 1000000 INFO @ Wed, 08 Dec 2021 20:23:51: 10000000 INFO @ Wed, 08 Dec 2021 20:23:55: 5000000 INFO @ Wed, 08 Dec 2021 20:23:56: 2000000 INFO @ Wed, 08 Dec 2021 20:23:59: 11000000 INFO @ Wed, 08 Dec 2021 20:24:05: 6000000 INFO @ Wed, 08 Dec 2021 20:24:06: 3000000 INFO @ Wed, 08 Dec 2021 20:24:06: 12000000 INFO @ Wed, 08 Dec 2021 20:24:14: 13000000 INFO @ Wed, 08 Dec 2021 20:24:15: 7000000 INFO @ Wed, 08 Dec 2021 20:24:16: 4000000 INFO @ Wed, 08 Dec 2021 20:24:21: 14000000 INFO @ Wed, 08 Dec 2021 20:24:25: 8000000 INFO @ Wed, 08 Dec 2021 20:24:26: 5000000 INFO @ Wed, 08 Dec 2021 20:24:29: 15000000 INFO @ Wed, 08 Dec 2021 20:24:35: 9000000 INFO @ Wed, 08 Dec 2021 20:24:36: 6000000 INFO @ Wed, 08 Dec 2021 20:24:36: 16000000 INFO @ Wed, 08 Dec 2021 20:24:44: 17000000 INFO @ Wed, 08 Dec 2021 20:24:44: 10000000 INFO @ Wed, 08 Dec 2021 20:24:45: 7000000 INFO @ Wed, 08 Dec 2021 20:24:51: 18000000 INFO @ Wed, 08 Dec 2021 20:24:54: 11000000 INFO @ Wed, 08 Dec 2021 20:24:55: 8000000 INFO @ Wed, 08 Dec 2021 20:24:59: 19000000 INFO @ Wed, 08 Dec 2021 20:25:04: 12000000 INFO @ Wed, 08 Dec 2021 20:25:06: 9000000 INFO @ Wed, 08 Dec 2021 20:25:07: 20000000 INFO @ Wed, 08 Dec 2021 20:25:14: 13000000 INFO @ Wed, 08 Dec 2021 20:25:15: 21000000 INFO @ Wed, 08 Dec 2021 20:25:16: 10000000 INFO @ Wed, 08 Dec 2021 20:25:22: 22000000 INFO @ Wed, 08 Dec 2021 20:25:24: 14000000 INFO @ Wed, 08 Dec 2021 20:25:26: 11000000 INFO @ Wed, 08 Dec 2021 20:25:30: 23000000 INFO @ Wed, 08 Dec 2021 20:25:34: 15000000 INFO @ Wed, 08 Dec 2021 20:25:35: 12000000 INFO @ Wed, 08 Dec 2021 20:25:37: 24000000 INFO @ Wed, 08 Dec 2021 20:25:45: 16000000 INFO @ Wed, 08 Dec 2021 20:25:45: 25000000 INFO @ Wed, 08 Dec 2021 20:25:45: 13000000 INFO @ Wed, 08 Dec 2021 20:25:52: 26000000 INFO @ Wed, 08 Dec 2021 20:25:54: 17000000 INFO @ Wed, 08 Dec 2021 20:25:56: 14000000 INFO @ Wed, 08 Dec 2021 20:26:00: 27000000 INFO @ Wed, 08 Dec 2021 20:26:03: 18000000 INFO @ Wed, 08 Dec 2021 20:26:06: 15000000 INFO @ Wed, 08 Dec 2021 20:26:08: 28000000 INFO @ Wed, 08 Dec 2021 20:26:13: 19000000 INFO @ Wed, 08 Dec 2021 20:26:15: 29000000 INFO @ Wed, 08 Dec 2021 20:26:16: 16000000 INFO @ Wed, 08 Dec 2021 20:26:23: 20000000 INFO @ Wed, 08 Dec 2021 20:26:23: 30000000 INFO @ Wed, 08 Dec 2021 20:26:25: 17000000 INFO @ Wed, 08 Dec 2021 20:26:31: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 20:26:33: 21000000 INFO @ Wed, 08 Dec 2021 20:26:35: 18000000 INFO @ Wed, 08 Dec 2021 20:26:38: 32000000 INFO @ Wed, 08 Dec 2021 20:26:41: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:26:41: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:26:41: #1 total tags in treatment: 14942014 INFO @ Wed, 08 Dec 2021 20:26:41: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:26:41: #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 20:26:41: #1 tags after filtering in treatment: 13816063 INFO @ Wed, 08 Dec 2021 20:26:41: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 20:26:41: #1 finished! INFO @ Wed, 08 Dec 2021 20:26:41: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:26:41: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:26:42: #2 number of paired peaks: 326 WARNING @ Wed, 08 Dec 2021 20:26:42: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Wed, 08 Dec 2021 20:26:42: start model_add_line... INFO @ Wed, 08 Dec 2021 20:26:42: start X-correlation... INFO @ Wed, 08 Dec 2021 20:26:42: end of X-cor INFO @ Wed, 08 Dec 2021 20:26:42: #2 finished! INFO @ Wed, 08 Dec 2021 20:26:42: #2 predicted fragment length is 133 bps INFO @ Wed, 08 Dec 2021 20:26:42: #2 alternative fragment length(s) may be 4,133 bps INFO @ Wed, 08 Dec 2021 20:26:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.05_model.r INFO @ Wed, 08 Dec 2021 20:26:42: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:26:42: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:26:43: 22000000 INFO @ Wed, 08 Dec 2021 20:26:45: 19000000 INFO @ Wed, 08 Dec 2021 20:26:54: 23000000 INFO @ Wed, 08 Dec 2021 20:26:55: 20000000 INFO @ Wed, 08 Dec 2021 20:27:04: 24000000 INFO @ Wed, 08 Dec 2021 20:27:05: 21000000 INFO @ Wed, 08 Dec 2021 20:27:07: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:27:13: 25000000 INFO @ Wed, 08 Dec 2021 20:27:15: 22000000 INFO @ Wed, 08 Dec 2021 20:27:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.05_peaks.xls INFO @ Wed, 08 Dec 2021 20:27:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:27:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.05_summits.bed INFO @ Wed, 08 Dec 2021 20:27:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (392 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:27:23: 26000000 INFO @ Wed, 08 Dec 2021 20:27:25: 23000000 INFO @ Wed, 08 Dec 2021 20:27:33: 27000000 INFO @ Wed, 08 Dec 2021 20:27:34: 24000000 INFO @ Wed, 08 Dec 2021 20:27:42: 28000000 INFO @ Wed, 08 Dec 2021 20:27:43: 25000000 INFO @ Wed, 08 Dec 2021 20:27:51: 29000000 INFO @ Wed, 08 Dec 2021 20:27:53: 26000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 20:28:01: 30000000 INFO @ Wed, 08 Dec 2021 20:28:03: 27000000 INFO @ Wed, 08 Dec 2021 20:28:10: 31000000 INFO @ Wed, 08 Dec 2021 20:28:13: 28000000 INFO @ Wed, 08 Dec 2021 20:28:20: 32000000 INFO @ Wed, 08 Dec 2021 20:28:23: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:28:23: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:28:23: #1 total tags in treatment: 14942014 INFO @ Wed, 08 Dec 2021 20:28:23: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:28:23: #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 20:28:23: #1 tags after filtering in treatment: 13816063 INFO @ Wed, 08 Dec 2021 20:28:23: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 20:28:23: #1 finished! INFO @ Wed, 08 Dec 2021 20:28:23: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:28:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:28:23: 29000000 INFO @ Wed, 08 Dec 2021 20:28:24: #2 number of paired peaks: 326 WARNING @ Wed, 08 Dec 2021 20:28:24: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Wed, 08 Dec 2021 20:28:24: start model_add_line... INFO @ Wed, 08 Dec 2021 20:28:24: start X-correlation... INFO @ Wed, 08 Dec 2021 20:28:24: end of X-cor INFO @ Wed, 08 Dec 2021 20:28:24: #2 finished! INFO @ Wed, 08 Dec 2021 20:28:24: #2 predicted fragment length is 133 bps INFO @ Wed, 08 Dec 2021 20:28:24: #2 alternative fragment length(s) may be 4,133 bps INFO @ Wed, 08 Dec 2021 20:28:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.10_model.r INFO @ Wed, 08 Dec 2021 20:28:24: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:28:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:28:33: 30000000 INFO @ Wed, 08 Dec 2021 20:28:42: 31000000 INFO @ Wed, 08 Dec 2021 20:28:49: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:28:52: 32000000 INFO @ Wed, 08 Dec 2021 20:28:54: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 20:28:54: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 20:28:54: #1 total tags in treatment: 14942014 INFO @ Wed, 08 Dec 2021 20:28:54: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 20:28:54: #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 20:28:55: #1 tags after filtering in treatment: 13816063 INFO @ Wed, 08 Dec 2021 20:28:55: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 20:28:55: #1 finished! INFO @ Wed, 08 Dec 2021 20:28:55: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 20:28:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 20:28:56: #2 number of paired peaks: 326 WARNING @ Wed, 08 Dec 2021 20:28:56: Fewer paired peaks (326) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 326 pairs to build model! INFO @ Wed, 08 Dec 2021 20:28:56: start model_add_line... INFO @ Wed, 08 Dec 2021 20:28:56: start X-correlation... INFO @ Wed, 08 Dec 2021 20:28:56: end of X-cor INFO @ Wed, 08 Dec 2021 20:28:56: #2 finished! INFO @ Wed, 08 Dec 2021 20:28:56: #2 predicted fragment length is 133 bps INFO @ Wed, 08 Dec 2021 20:28:56: #2 alternative fragment length(s) may be 4,133 bps INFO @ Wed, 08 Dec 2021 20:28:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.20_model.r INFO @ Wed, 08 Dec 2021 20:28:56: #3 Call peaks... INFO @ Wed, 08 Dec 2021 20:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 20:29:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.10_peaks.xls INFO @ Wed, 08 Dec 2021 20:29:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:29:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.10_summits.bed INFO @ Wed, 08 Dec 2021 20:29:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (311 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 20:29:21: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 20:29:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.20_peaks.xls INFO @ Wed, 08 Dec 2021 20:29:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 20:29:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX8976701/SRX8976701.20_summits.bed INFO @ Wed, 08 Dec 2021 20:29:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (207 records, 4 fields): 8 millis CompletedMACS2peakCalling