Job ID = 14158800 SRX = SRX10342583 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: 00:15:16 20855837 reads; of these: 20855837 (100.00%) were paired; of these: 4601671 (22.06%) aligned concordantly 0 times 13953486 (66.90%) aligned concordantly exactly 1 time 2300680 (11.03%) aligned concordantly >1 times ---- 4601671 pairs aligned concordantly 0 times; of these: 3495461 (75.96%) aligned discordantly 1 time ---- 1106210 pairs aligned 0 times concordantly or discordantly; of these: 2212420 mates make up the pairs; of these: 776775 (35.11%) aligned 0 times 566725 (25.62%) aligned exactly 1 time 868920 (39.27%) aligned >1 times 98.14% overall alignment rate Time searching: 00:15:16 Overall time: 00:15:16 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] 1504048 / 19730599 = 0.0762 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 18:23:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.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 18:23:31: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:23:31: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:23:36: 1000000 INFO @ Wed, 08 Dec 2021 18:23:40: 2000000 INFO @ Wed, 08 Dec 2021 18:23:44: 3000000 INFO @ Wed, 08 Dec 2021 18:23:48: 4000000 INFO @ Wed, 08 Dec 2021 18:23:53: 5000000 INFO @ Wed, 08 Dec 2021 18:23:57: 6000000 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 18:24:01: 7000000 INFO @ Wed, 08 Dec 2021 18:24:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.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 18:24:01: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:24:01: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:24:05: 8000000 INFO @ Wed, 08 Dec 2021 18:24:06: 1000000 INFO @ Wed, 08 Dec 2021 18:24:10: 9000000 INFO @ Wed, 08 Dec 2021 18:24:11: 2000000 INFO @ Wed, 08 Dec 2021 18:24:14: 10000000 INFO @ Wed, 08 Dec 2021 18:24:16: 3000000 INFO @ Wed, 08 Dec 2021 18:24:19: 11000000 INFO @ Wed, 08 Dec 2021 18:24:21: 4000000 INFO @ Wed, 08 Dec 2021 18:24:23: 12000000 INFO @ Wed, 08 Dec 2021 18:24:26: 5000000 INFO @ Wed, 08 Dec 2021 18:24:28: 13000000 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 18:24:31: 6000000 INFO @ Wed, 08 Dec 2021 18:24:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.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 18:24:31: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:24:31: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:24:32: 14000000 INFO @ Wed, 08 Dec 2021 18:24:36: 1000000 INFO @ Wed, 08 Dec 2021 18:24:36: 7000000 INFO @ Wed, 08 Dec 2021 18:24:37: 15000000 INFO @ Wed, 08 Dec 2021 18:24:40: 2000000 INFO @ Wed, 08 Dec 2021 18:24:41: 8000000 INFO @ Wed, 08 Dec 2021 18:24:42: 16000000 INFO @ Wed, 08 Dec 2021 18:24:45: 3000000 INFO @ Wed, 08 Dec 2021 18:24:46: 9000000 INFO @ Wed, 08 Dec 2021 18:24:46: 17000000 INFO @ Wed, 08 Dec 2021 18:24:49: 4000000 INFO @ Wed, 08 Dec 2021 18:24:51: 18000000 INFO @ Wed, 08 Dec 2021 18:24:51: 10000000 INFO @ Wed, 08 Dec 2021 18:24:54: 5000000 INFO @ Wed, 08 Dec 2021 18:24:55: 19000000 INFO @ Wed, 08 Dec 2021 18:24:56: 11000000 INFO @ Wed, 08 Dec 2021 18:24:59: 6000000 INFO @ Wed, 08 Dec 2021 18:25:00: 20000000 INFO @ Wed, 08 Dec 2021 18:25:01: 12000000 INFO @ Wed, 08 Dec 2021 18:25:03: 7000000 INFO @ Wed, 08 Dec 2021 18:25:04: 21000000 INFO @ Wed, 08 Dec 2021 18:25:06: 13000000 INFO @ Wed, 08 Dec 2021 18:25:08: 8000000 INFO @ Wed, 08 Dec 2021 18:25:09: 22000000 INFO @ Wed, 08 Dec 2021 18:25:11: 14000000 INFO @ Wed, 08 Dec 2021 18:25:13: 9000000 INFO @ Wed, 08 Dec 2021 18:25:14: 23000000 INFO @ Wed, 08 Dec 2021 18:25:16: 15000000 INFO @ Wed, 08 Dec 2021 18:25:17: 10000000 INFO @ Wed, 08 Dec 2021 18:25:18: 24000000 INFO @ Wed, 08 Dec 2021 18:25:21: 16000000 INFO @ Wed, 08 Dec 2021 18:25:22: 11000000 INFO @ Wed, 08 Dec 2021 18:25:23: 25000000 INFO @ Wed, 08 Dec 2021 18:25:26: 17000000 INFO @ Wed, 08 Dec 2021 18:25:26: 12000000 INFO @ Wed, 08 Dec 2021 18:25:28: 26000000 INFO @ Wed, 08 Dec 2021 18:25:31: 13000000 INFO @ Wed, 08 Dec 2021 18:25:31: 18000000 INFO @ Wed, 08 Dec 2021 18:25:32: 27000000 INFO @ Wed, 08 Dec 2021 18:25:35: 14000000 INFO @ Wed, 08 Dec 2021 18:25:36: 19000000 INFO @ Wed, 08 Dec 2021 18:25:37: 28000000 INFO @ Wed, 08 Dec 2021 18:25:40: 15000000 INFO @ Wed, 08 Dec 2021 18:25:41: 29000000 INFO @ Wed, 08 Dec 2021 18:25:41: 20000000 INFO @ Wed, 08 Dec 2021 18:25:45: 16000000 INFO @ Wed, 08 Dec 2021 18:25:46: 30000000 INFO @ Wed, 08 Dec 2021 18:25:46: 21000000 INFO @ Wed, 08 Dec 2021 18:25:49: 17000000 INFO @ Wed, 08 Dec 2021 18:25:50: 31000000 INFO @ Wed, 08 Dec 2021 18:25:52: 22000000 INFO @ Wed, 08 Dec 2021 18:25:54: 18000000 INFO @ Wed, 08 Dec 2021 18:25:55: 32000000 INFO @ Wed, 08 Dec 2021 18:25:57: 23000000 INFO @ Wed, 08 Dec 2021 18:25:58: 19000000 INFO @ Wed, 08 Dec 2021 18:26:00: 33000000 INFO @ Wed, 08 Dec 2021 18:26:02: 24000000 INFO @ Wed, 08 Dec 2021 18:26:03: 20000000 INFO @ Wed, 08 Dec 2021 18:26:04: 34000000 INFO @ Wed, 08 Dec 2021 18:26:07: 25000000 INFO @ Wed, 08 Dec 2021 18:26:07: 21000000 INFO @ Wed, 08 Dec 2021 18:26:09: 35000000 INFO @ Wed, 08 Dec 2021 18:26:12: 26000000 INFO @ Wed, 08 Dec 2021 18:26:12: 22000000 INFO @ Wed, 08 Dec 2021 18:26:13: 36000000 INFO @ Wed, 08 Dec 2021 18:26:17: 27000000 INFO @ Wed, 08 Dec 2021 18:26:17: 23000000 INFO @ Wed, 08 Dec 2021 18:26:18: 37000000 INFO @ Wed, 08 Dec 2021 18:26:21: 24000000 INFO @ Wed, 08 Dec 2021 18:26:22: 28000000 INFO @ Wed, 08 Dec 2021 18:26:22: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:26:22: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:26:22: #1 total tags in treatment: 14959150 INFO @ Wed, 08 Dec 2021 18:26:22: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:26:22: #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 18:26:22: #1 tags after filtering in treatment: 13533261 INFO @ Wed, 08 Dec 2021 18:26:22: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 08 Dec 2021 18:26:22: #1 finished! INFO @ Wed, 08 Dec 2021 18:26:22: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:26:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:26:23: #2 number of paired peaks: 414 WARNING @ Wed, 08 Dec 2021 18:26:23: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Wed, 08 Dec 2021 18:26:23: start model_add_line... INFO @ Wed, 08 Dec 2021 18:26:23: start X-correlation... INFO @ Wed, 08 Dec 2021 18:26:23: end of X-cor INFO @ Wed, 08 Dec 2021 18:26:23: #2 finished! INFO @ Wed, 08 Dec 2021 18:26:23: #2 predicted fragment length is 110 bps INFO @ Wed, 08 Dec 2021 18:26:23: #2 alternative fragment length(s) may be 3,110,122 bps INFO @ Wed, 08 Dec 2021 18:26:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.05_model.r INFO @ Wed, 08 Dec 2021 18:26:23: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:26:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:26:26: 25000000 INFO @ Wed, 08 Dec 2021 18:26:27: 29000000 INFO @ Wed, 08 Dec 2021 18:26:30: 26000000 INFO @ Wed, 08 Dec 2021 18:26:32: 30000000 INFO @ Wed, 08 Dec 2021 18:26:35: 27000000 INFO @ Wed, 08 Dec 2021 18:26:37: 31000000 INFO @ Wed, 08 Dec 2021 18:26:39: 28000000 INFO @ Wed, 08 Dec 2021 18:26:42: 32000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:26:44: 29000000 INFO @ Wed, 08 Dec 2021 18:26:47: 33000000 INFO @ Wed, 08 Dec 2021 18:26:48: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:26:49: 30000000 INFO @ Wed, 08 Dec 2021 18:26:52: 34000000 INFO @ Wed, 08 Dec 2021 18:26:53: 31000000 INFO @ Wed, 08 Dec 2021 18:26:57: 35000000 INFO @ Wed, 08 Dec 2021 18:26:58: 32000000 INFO @ Wed, 08 Dec 2021 18:27:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:27:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:27:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.05_summits.bed INFO @ Wed, 08 Dec 2021 18:27:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (459 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:27:02: 36000000 INFO @ Wed, 08 Dec 2021 18:27:03: 33000000 INFO @ Wed, 08 Dec 2021 18:27:07: 37000000 INFO @ Wed, 08 Dec 2021 18:27:07: 34000000 INFO @ Wed, 08 Dec 2021 18:27:11: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:27:11: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:27:11: #1 total tags in treatment: 14959150 INFO @ Wed, 08 Dec 2021 18:27:11: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:27:11: #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 18:27:11: #1 tags after filtering in treatment: 13533261 INFO @ Wed, 08 Dec 2021 18:27:11: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 08 Dec 2021 18:27:11: #1 finished! INFO @ Wed, 08 Dec 2021 18:27:11: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:27:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:27:12: 35000000 INFO @ Wed, 08 Dec 2021 18:27:12: #2 number of paired peaks: 414 WARNING @ Wed, 08 Dec 2021 18:27:12: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Wed, 08 Dec 2021 18:27:12: start model_add_line... INFO @ Wed, 08 Dec 2021 18:27:12: start X-correlation... INFO @ Wed, 08 Dec 2021 18:27:12: end of X-cor INFO @ Wed, 08 Dec 2021 18:27:12: #2 finished! INFO @ Wed, 08 Dec 2021 18:27:12: #2 predicted fragment length is 110 bps INFO @ Wed, 08 Dec 2021 18:27:12: #2 alternative fragment length(s) may be 3,110,122 bps INFO @ Wed, 08 Dec 2021 18:27:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.10_model.r INFO @ Wed, 08 Dec 2021 18:27:12: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:27:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:27:16: 36000000 INFO @ Wed, 08 Dec 2021 18:27:21: 37000000 INFO @ Wed, 08 Dec 2021 18:27:25: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:27:25: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:27:25: #1 total tags in treatment: 14959150 INFO @ Wed, 08 Dec 2021 18:27:25: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:27:25: #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 18:27:25: #1 tags after filtering in treatment: 13533261 INFO @ Wed, 08 Dec 2021 18:27:25: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 08 Dec 2021 18:27:25: #1 finished! INFO @ Wed, 08 Dec 2021 18:27:25: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:27:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:27:26: #2 number of paired peaks: 414 WARNING @ Wed, 08 Dec 2021 18:27:26: Fewer paired peaks (414) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 414 pairs to build model! INFO @ Wed, 08 Dec 2021 18:27:26: start model_add_line... INFO @ Wed, 08 Dec 2021 18:27:26: start X-correlation... INFO @ Wed, 08 Dec 2021 18:27:26: end of X-cor INFO @ Wed, 08 Dec 2021 18:27:26: #2 finished! INFO @ Wed, 08 Dec 2021 18:27:26: #2 predicted fragment length is 110 bps INFO @ Wed, 08 Dec 2021 18:27:26: #2 alternative fragment length(s) may be 3,110,122 bps INFO @ Wed, 08 Dec 2021 18:27:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.20_model.r INFO @ Wed, 08 Dec 2021 18:27:26: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:27:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:27:38: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:27:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:27:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:27:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.10_summits.bed INFO @ Wed, 08 Dec 2021 18:27:50: Done! INFO @ Wed, 08 Dec 2021 18:27:50: #3 Call peaks for each chromosome... pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (345 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:28:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:28:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:28:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342583/SRX10342583.20_summits.bed INFO @ Wed, 08 Dec 2021 18:28:02: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (216 records, 4 fields): 13 millis CompletedMACS2peakCalling