Job ID = 14158765 SRX = SRX10342575 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: 00:47:58 33852201 reads; of these: 33852201 (100.00%) were paired; of these: 6005221 (17.74%) aligned concordantly 0 times 17601961 (52.00%) aligned concordantly exactly 1 time 10245019 (30.26%) aligned concordantly >1 times ---- 6005221 pairs aligned concordantly 0 times; of these: 1963584 (32.70%) aligned discordantly 1 time ---- 4041637 pairs aligned 0 times concordantly or discordantly; of these: 8083274 mates make up the pairs; of these: 4670602 (57.78%) aligned 0 times 1485138 (18.37%) aligned exactly 1 time 1927534 (23.85%) aligned >1 times 93.10% overall alignment rate Time searching: 00:47:58 Overall time: 00:47:58 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 28 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] 6923358 / 29535397 = 0.2344 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 18:46:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.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 18:46:23: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:46:23: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:46:27: 1000000 INFO @ Wed, 08 Dec 2021 18:46:32: 2000000 INFO @ Wed, 08 Dec 2021 18:46:37: 3000000 INFO @ Wed, 08 Dec 2021 18:46:42: 4000000 INFO @ Wed, 08 Dec 2021 18:46:46: 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 18:46:51: 6000000 INFO @ Wed, 08 Dec 2021 18:46:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.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 18:46:52: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:46:52: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:46:56: 7000000 INFO @ Wed, 08 Dec 2021 18:46:57: 1000000 INFO @ Wed, 08 Dec 2021 18:47:02: 8000000 INFO @ Wed, 08 Dec 2021 18:47:03: 2000000 INFO @ Wed, 08 Dec 2021 18:47:07: 9000000 INFO @ Wed, 08 Dec 2021 18:47:08: 3000000 INFO @ Wed, 08 Dec 2021 18:47:12: 10000000 INFO @ Wed, 08 Dec 2021 18:47:13: 4000000 INFO @ Wed, 08 Dec 2021 18:47:18: 11000000 INFO @ Wed, 08 Dec 2021 18:47:19: 5000000 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 18:47:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.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 18:47:23: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:47:23: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:47:23: 12000000 INFO @ Wed, 08 Dec 2021 18:47:24: 6000000 INFO @ Wed, 08 Dec 2021 18:47:28: 13000000 INFO @ Wed, 08 Dec 2021 18:47:29: 1000000 INFO @ Wed, 08 Dec 2021 18:47:30: 7000000 INFO @ Wed, 08 Dec 2021 18:47:34: 14000000 INFO @ Wed, 08 Dec 2021 18:47:34: 2000000 INFO @ Wed, 08 Dec 2021 18:47:35: 8000000 INFO @ Wed, 08 Dec 2021 18:47:40: 15000000 INFO @ Wed, 08 Dec 2021 18:47:40: 3000000 INFO @ Wed, 08 Dec 2021 18:47:41: 9000000 INFO @ Wed, 08 Dec 2021 18:47:45: 16000000 INFO @ Wed, 08 Dec 2021 18:47:45: 4000000 INFO @ Wed, 08 Dec 2021 18:47:46: 10000000 INFO @ Wed, 08 Dec 2021 18:47:51: 17000000 INFO @ Wed, 08 Dec 2021 18:47:51: 5000000 INFO @ Wed, 08 Dec 2021 18:47:52: 11000000 INFO @ Wed, 08 Dec 2021 18:47:56: 18000000 INFO @ Wed, 08 Dec 2021 18:47:57: 6000000 INFO @ Wed, 08 Dec 2021 18:47:57: 12000000 INFO @ Wed, 08 Dec 2021 18:48:02: 19000000 INFO @ Wed, 08 Dec 2021 18:48:02: 7000000 INFO @ Wed, 08 Dec 2021 18:48:03: 13000000 INFO @ Wed, 08 Dec 2021 18:48:08: 20000000 INFO @ Wed, 08 Dec 2021 18:48:08: 8000000 INFO @ Wed, 08 Dec 2021 18:48:09: 14000000 INFO @ Wed, 08 Dec 2021 18:48:13: 21000000 INFO @ Wed, 08 Dec 2021 18:48:13: 9000000 INFO @ Wed, 08 Dec 2021 18:48:14: 15000000 INFO @ Wed, 08 Dec 2021 18:48:19: 22000000 INFO @ Wed, 08 Dec 2021 18:48:19: 10000000 INFO @ Wed, 08 Dec 2021 18:48:19: 16000000 INFO @ Wed, 08 Dec 2021 18:48:24: 23000000 INFO @ Wed, 08 Dec 2021 18:48:24: 11000000 INFO @ Wed, 08 Dec 2021 18:48:25: 17000000 INFO @ Wed, 08 Dec 2021 18:48:29: 24000000 INFO @ Wed, 08 Dec 2021 18:48:30: 12000000 INFO @ Wed, 08 Dec 2021 18:48:30: 18000000 INFO @ Wed, 08 Dec 2021 18:48:35: 25000000 INFO @ Wed, 08 Dec 2021 18:48:35: 13000000 INFO @ Wed, 08 Dec 2021 18:48:36: 19000000 INFO @ Wed, 08 Dec 2021 18:48:40: 14000000 INFO @ Wed, 08 Dec 2021 18:48:40: 26000000 INFO @ Wed, 08 Dec 2021 18:48:41: 20000000 INFO @ Wed, 08 Dec 2021 18:48:46: 15000000 INFO @ Wed, 08 Dec 2021 18:48:46: 27000000 INFO @ Wed, 08 Dec 2021 18:48:46: 21000000 INFO @ Wed, 08 Dec 2021 18:48:51: 16000000 INFO @ Wed, 08 Dec 2021 18:48:52: 28000000 INFO @ Wed, 08 Dec 2021 18:48:52: 22000000 INFO @ Wed, 08 Dec 2021 18:48:57: 17000000 INFO @ Wed, 08 Dec 2021 18:48:57: 29000000 INFO @ Wed, 08 Dec 2021 18:48:57: 23000000 INFO @ Wed, 08 Dec 2021 18:49:02: 18000000 INFO @ Wed, 08 Dec 2021 18:49:03: 30000000 INFO @ Wed, 08 Dec 2021 18:49:03: 24000000 INFO @ Wed, 08 Dec 2021 18:49:08: 19000000 INFO @ Wed, 08 Dec 2021 18:49:08: 25000000 INFO @ Wed, 08 Dec 2021 18:49:08: 31000000 INFO @ Wed, 08 Dec 2021 18:49:13: 20000000 INFO @ Wed, 08 Dec 2021 18:49:13: 26000000 INFO @ Wed, 08 Dec 2021 18:49:13: 32000000 INFO @ Wed, 08 Dec 2021 18:49:19: 21000000 INFO @ Wed, 08 Dec 2021 18:49:19: 27000000 INFO @ Wed, 08 Dec 2021 18:49:19: 33000000 INFO @ Wed, 08 Dec 2021 18:49:24: 34000000 INFO @ Wed, 08 Dec 2021 18:49:24: 28000000 INFO @ Wed, 08 Dec 2021 18:49:24: 22000000 INFO @ Wed, 08 Dec 2021 18:49:30: 35000000 INFO @ Wed, 08 Dec 2021 18:49:30: 23000000 INFO @ Wed, 08 Dec 2021 18:49:30: 29000000 INFO @ Wed, 08 Dec 2021 18:49:35: 36000000 INFO @ Wed, 08 Dec 2021 18:49:35: 24000000 INFO @ Wed, 08 Dec 2021 18:49:35: 30000000 INFO @ Wed, 08 Dec 2021 18:49:41: 31000000 INFO @ Wed, 08 Dec 2021 18:49:41: 25000000 INFO @ Wed, 08 Dec 2021 18:49:41: 37000000 INFO @ Wed, 08 Dec 2021 18:49:46: 32000000 INFO @ Wed, 08 Dec 2021 18:49:46: 26000000 INFO @ Wed, 08 Dec 2021 18:49:46: 38000000 INFO @ Wed, 08 Dec 2021 18:49:51: 33000000 INFO @ Wed, 08 Dec 2021 18:49:51: 27000000 INFO @ Wed, 08 Dec 2021 18:49:52: 39000000 INFO @ Wed, 08 Dec 2021 18:49:57: 34000000 INFO @ Wed, 08 Dec 2021 18:49:57: 28000000 INFO @ Wed, 08 Dec 2021 18:49:57: 40000000 INFO @ Wed, 08 Dec 2021 18:50:02: 35000000 INFO @ Wed, 08 Dec 2021 18:50:02: 29000000 INFO @ Wed, 08 Dec 2021 18:50:02: 41000000 INFO @ Wed, 08 Dec 2021 18:50:07: 36000000 INFO @ Wed, 08 Dec 2021 18:50:08: 30000000 INFO @ Wed, 08 Dec 2021 18:50:08: 42000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:50:13: 37000000 INFO @ Wed, 08 Dec 2021 18:50:13: 31000000 INFO @ Wed, 08 Dec 2021 18:50:13: 43000000 INFO @ Wed, 08 Dec 2021 18:50:18: 38000000 INFO @ Wed, 08 Dec 2021 18:50:19: 32000000 INFO @ Wed, 08 Dec 2021 18:50:19: 44000000 INFO @ Wed, 08 Dec 2021 18:50:24: 39000000 INFO @ Wed, 08 Dec 2021 18:50:24: 33000000 INFO @ Wed, 08 Dec 2021 18:50:24: 45000000 INFO @ Wed, 08 Dec 2021 18:50:29: 40000000 INFO @ Wed, 08 Dec 2021 18:50:29: 34000000 INFO @ Wed, 08 Dec 2021 18:50:29: 46000000 INFO @ Wed, 08 Dec 2021 18:50:34: 41000000 INFO @ Wed, 08 Dec 2021 18:50:35: 35000000 INFO @ Wed, 08 Dec 2021 18:50:35: 47000000 INFO @ Wed, 08 Dec 2021 18:50:40: 42000000 INFO @ Wed, 08 Dec 2021 18:50:40: 36000000 INFO @ Wed, 08 Dec 2021 18:50:40: 48000000 INFO @ Wed, 08 Dec 2021 18:50:45: 43000000 INFO @ Wed, 08 Dec 2021 18:50:46: 37000000 INFO @ Wed, 08 Dec 2021 18:50:46: 49000000 INFO @ Wed, 08 Dec 2021 18:50:47: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:50:47: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:50:47: #1 total tags in treatment: 21148539 INFO @ Wed, 08 Dec 2021 18:50:47: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:50:47: #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 18:50:47: #1 tags after filtering in treatment: 15190351 INFO @ Wed, 08 Dec 2021 18:50:47: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 08 Dec 2021 18:50:47: #1 finished! INFO @ Wed, 08 Dec 2021 18:50:47: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:50:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:50:48: #2 number of paired peaks: 1170 INFO @ Wed, 08 Dec 2021 18:50:48: start model_add_line... INFO @ Wed, 08 Dec 2021 18:50:48: start X-correlation... INFO @ Wed, 08 Dec 2021 18:50:48: end of X-cor INFO @ Wed, 08 Dec 2021 18:50:48: #2 finished! INFO @ Wed, 08 Dec 2021 18:50:48: #2 predicted fragment length is 151 bps INFO @ Wed, 08 Dec 2021 18:50:48: #2 alternative fragment length(s) may be 4,151 bps INFO @ Wed, 08 Dec 2021 18:50:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.05_model.r INFO @ Wed, 08 Dec 2021 18:50:49: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:50:49: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:50:50: 44000000 INFO @ Wed, 08 Dec 2021 18:50:51: 38000000 INFO @ Wed, 08 Dec 2021 18:50:56: 45000000 INFO @ Wed, 08 Dec 2021 18:50:56: 39000000 INFO @ Wed, 08 Dec 2021 18:51:01: 46000000 INFO @ Wed, 08 Dec 2021 18:51:02: 40000000 INFO @ Wed, 08 Dec 2021 18:51:06: 47000000 INFO @ Wed, 08 Dec 2021 18:51:07: 41000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:51:12: 48000000 INFO @ Wed, 08 Dec 2021 18:51:12: 42000000 INFO @ Wed, 08 Dec 2021 18:51:17: 49000000 INFO @ Wed, 08 Dec 2021 18:51:18: 43000000 INFO @ Wed, 08 Dec 2021 18:51:18: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:51:18: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:51:18: #1 total tags in treatment: 21148539 INFO @ Wed, 08 Dec 2021 18:51:18: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:51:18: #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 18:51:18: #1 tags after filtering in treatment: 15190351 INFO @ Wed, 08 Dec 2021 18:51:18: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 08 Dec 2021 18:51:18: #1 finished! INFO @ Wed, 08 Dec 2021 18:51:18: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:51:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:51:19: #2 number of paired peaks: 1170 INFO @ Wed, 08 Dec 2021 18:51:19: start model_add_line... INFO @ Wed, 08 Dec 2021 18:51:20: start X-correlation... INFO @ Wed, 08 Dec 2021 18:51:20: end of X-cor INFO @ Wed, 08 Dec 2021 18:51:20: #2 finished! INFO @ Wed, 08 Dec 2021 18:51:20: #2 predicted fragment length is 151 bps INFO @ Wed, 08 Dec 2021 18:51:20: #2 alternative fragment length(s) may be 4,151 bps INFO @ Wed, 08 Dec 2021 18:51:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.10_model.r INFO @ Wed, 08 Dec 2021 18:51:20: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:51:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:51:21: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:51:23: 44000000 INFO @ Wed, 08 Dec 2021 18:51:28: 45000000 INFO @ Wed, 08 Dec 2021 18:51:33: 46000000 INFO @ Wed, 08 Dec 2021 18:51:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:51:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:51:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.05_summits.bed INFO @ Wed, 08 Dec 2021 18:51:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4132 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:51:38: 47000000 INFO @ Wed, 08 Dec 2021 18:51:42: 48000000 INFO @ Wed, 08 Dec 2021 18:51:47: 49000000 INFO @ Wed, 08 Dec 2021 18:51:48: #1 tag size is determined as 51 bps INFO @ Wed, 08 Dec 2021 18:51:48: #1 tag size = 51 INFO @ Wed, 08 Dec 2021 18:51:48: #1 total tags in treatment: 21148539 INFO @ Wed, 08 Dec 2021 18:51:48: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:51:48: #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 18:51:49: #1 tags after filtering in treatment: 15190351 INFO @ Wed, 08 Dec 2021 18:51:49: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 08 Dec 2021 18:51:49: #1 finished! INFO @ Wed, 08 Dec 2021 18:51:49: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:51:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:51:50: #2 number of paired peaks: 1170 INFO @ Wed, 08 Dec 2021 18:51:50: start model_add_line... INFO @ Wed, 08 Dec 2021 18:51:50: start X-correlation... INFO @ Wed, 08 Dec 2021 18:51:50: end of X-cor INFO @ Wed, 08 Dec 2021 18:51:50: #2 finished! INFO @ Wed, 08 Dec 2021 18:51:50: #2 predicted fragment length is 151 bps INFO @ Wed, 08 Dec 2021 18:51:50: #2 alternative fragment length(s) may be 4,151 bps INFO @ Wed, 08 Dec 2021 18:51:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.20_model.r INFO @ Wed, 08 Dec 2021 18:51:50: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:51:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:51:52: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:52:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:52:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:52:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.10_summits.bed INFO @ Wed, 08 Dec 2021 18:52:06: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2152 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:52:21: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:52:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:52:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:52:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342575/SRX10342575.20_summits.bed INFO @ Wed, 08 Dec 2021 18:52:36: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (970 records, 4 fields): 36 millis CompletedMACS2peakCalling