Job ID = 14158368 SRX = SRX10342599 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 10834162 spots for SRR13964654/SRR13964654.sra Written 10834162 spots for SRR13964654/SRR13964654.sra Read 11981591 spots for SRR13964655/SRR13964655.sra Written 11981591 spots for SRR13964655/SRR13964655.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158949 ("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: 00:16:03 22815753 reads; of these: 22815753 (100.00%) were paired; of these: 5931731 (26.00%) aligned concordantly 0 times 14821469 (64.96%) aligned concordantly exactly 1 time 2062553 (9.04%) aligned concordantly >1 times ---- 5931731 pairs aligned concordantly 0 times; of these: 4326278 (72.93%) aligned discordantly 1 time ---- 1605453 pairs aligned 0 times concordantly or discordantly; of these: 3210906 mates make up the pairs; of these: 1519057 (47.31%) aligned 0 times 696449 (21.69%) aligned exactly 1 time 995400 (31.00%) aligned >1 times 96.67% overall alignment rate Time searching: 00:16:03 Overall time: 00:16:03 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] 2369499 / 21196361 = 0.1118 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 16:47:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.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 16:47:51: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:47:51: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:47:56: 1000000 INFO @ Wed, 08 Dec 2021 16:48:01: 2000000 INFO @ Wed, 08 Dec 2021 16:48:05: 3000000 INFO @ Wed, 08 Dec 2021 16:48:10: 4000000 INFO @ Wed, 08 Dec 2021 16:48:14: 5000000 INFO @ Wed, 08 Dec 2021 16:48:19: 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 16:48:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.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 16:48:21: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:48:21: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:48:23: 7000000 INFO @ Wed, 08 Dec 2021 16:48:28: 1000000 INFO @ Wed, 08 Dec 2021 16:48:29: 8000000 INFO @ Wed, 08 Dec 2021 16:48:34: 2000000 INFO @ Wed, 08 Dec 2021 16:48:34: 9000000 INFO @ Wed, 08 Dec 2021 16:48:39: 10000000 INFO @ Wed, 08 Dec 2021 16:48:40: 3000000 INFO @ Wed, 08 Dec 2021 16:48:45: 11000000 INFO @ Wed, 08 Dec 2021 16:48:46: 4000000 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 16:48:50: 12000000 INFO @ Wed, 08 Dec 2021 16:48:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.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 16:48:51: #1 read tag files... INFO @ Wed, 08 Dec 2021 16:48:51: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 16:48:53: 5000000 INFO @ Wed, 08 Dec 2021 16:48:55: 13000000 INFO @ Wed, 08 Dec 2021 16:48:57: 1000000 INFO @ Wed, 08 Dec 2021 16:48:59: 6000000 INFO @ Wed, 08 Dec 2021 16:49:01: 14000000 INFO @ Wed, 08 Dec 2021 16:49:03: 2000000 INFO @ Wed, 08 Dec 2021 16:49:05: 7000000 INFO @ Wed, 08 Dec 2021 16:49:07: 15000000 INFO @ Wed, 08 Dec 2021 16:49:08: 3000000 INFO @ Wed, 08 Dec 2021 16:49:11: 8000000 INFO @ Wed, 08 Dec 2021 16:49:12: 16000000 INFO @ Wed, 08 Dec 2021 16:49:14: 4000000 INFO @ Wed, 08 Dec 2021 16:49:17: 9000000 INFO @ Wed, 08 Dec 2021 16:49:18: 17000000 INFO @ Wed, 08 Dec 2021 16:49:20: 5000000 INFO @ Wed, 08 Dec 2021 16:49:23: 10000000 INFO @ Wed, 08 Dec 2021 16:49:23: 18000000 INFO @ Wed, 08 Dec 2021 16:49:25: 6000000 INFO @ Wed, 08 Dec 2021 16:49:29: 11000000 INFO @ Wed, 08 Dec 2021 16:49:29: 19000000 INFO @ Wed, 08 Dec 2021 16:49:31: 7000000 INFO @ Wed, 08 Dec 2021 16:49:35: 20000000 INFO @ Wed, 08 Dec 2021 16:49:35: 12000000 INFO @ Wed, 08 Dec 2021 16:49:36: 8000000 INFO @ Wed, 08 Dec 2021 16:49:40: 21000000 INFO @ Wed, 08 Dec 2021 16:49:41: 13000000 INFO @ Wed, 08 Dec 2021 16:49:42: 9000000 INFO @ Wed, 08 Dec 2021 16:49:46: 22000000 INFO @ Wed, 08 Dec 2021 16:49:47: 14000000 INFO @ Wed, 08 Dec 2021 16:49:48: 10000000 INFO @ Wed, 08 Dec 2021 16:49:52: 23000000 INFO @ Wed, 08 Dec 2021 16:49:53: 15000000 INFO @ Wed, 08 Dec 2021 16:49:53: 11000000 INFO @ Wed, 08 Dec 2021 16:49:57: 24000000 INFO @ Wed, 08 Dec 2021 16:49:59: 16000000 INFO @ Wed, 08 Dec 2021 16:49:59: 12000000 INFO @ Wed, 08 Dec 2021 16:50:03: 25000000 INFO @ Wed, 08 Dec 2021 16:50:04: 13000000 INFO @ Wed, 08 Dec 2021 16:50:05: 17000000 INFO @ Wed, 08 Dec 2021 16:50:08: 26000000 INFO @ Wed, 08 Dec 2021 16:50:10: 14000000 INFO @ Wed, 08 Dec 2021 16:50:11: 18000000 INFO @ Wed, 08 Dec 2021 16:50:14: 27000000 INFO @ Wed, 08 Dec 2021 16:50:16: 15000000 INFO @ Wed, 08 Dec 2021 16:50:17: 19000000 INFO @ Wed, 08 Dec 2021 16:50:20: 28000000 INFO @ Wed, 08 Dec 2021 16:50:21: 16000000 INFO @ Wed, 08 Dec 2021 16:50:23: 20000000 INFO @ Wed, 08 Dec 2021 16:50:25: 29000000 INFO @ Wed, 08 Dec 2021 16:50:27: 17000000 INFO @ Wed, 08 Dec 2021 16:50:29: 21000000 INFO @ Wed, 08 Dec 2021 16:50:31: 30000000 INFO @ Wed, 08 Dec 2021 16:50:33: 18000000 INFO @ Wed, 08 Dec 2021 16:50:35: 22000000 INFO @ Wed, 08 Dec 2021 16:50:36: 31000000 INFO @ Wed, 08 Dec 2021 16:50:38: 19000000 INFO @ Wed, 08 Dec 2021 16:50:41: 23000000 INFO @ Wed, 08 Dec 2021 16:50:42: 32000000 INFO @ Wed, 08 Dec 2021 16:50:44: 20000000 INFO @ Wed, 08 Dec 2021 16:50:47: 24000000 INFO @ Wed, 08 Dec 2021 16:50:48: 33000000 INFO @ Wed, 08 Dec 2021 16:50:49: 21000000 INFO @ Wed, 08 Dec 2021 16:50:53: 25000000 INFO @ Wed, 08 Dec 2021 16:50:53: 34000000 INFO @ Wed, 08 Dec 2021 16:50:55: 22000000 INFO @ Wed, 08 Dec 2021 16:50:59: 26000000 INFO @ Wed, 08 Dec 2021 16:50:59: 35000000 INFO @ Wed, 08 Dec 2021 16:51:00: 23000000 INFO @ Wed, 08 Dec 2021 16:51:05: 27000000 INFO @ Wed, 08 Dec 2021 16:51:05: 36000000 INFO @ Wed, 08 Dec 2021 16:51:06: 24000000 INFO @ Wed, 08 Dec 2021 16:51:10: 37000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 16:51:10: 28000000 INFO @ Wed, 08 Dec 2021 16:51:12: 25000000 INFO @ Wed, 08 Dec 2021 16:51:16: 38000000 INFO @ Wed, 08 Dec 2021 16:51:16: 29000000 INFO @ Wed, 08 Dec 2021 16:51:17: 26000000 INFO @ Wed, 08 Dec 2021 16:51:22: 39000000 INFO @ Wed, 08 Dec 2021 16:51:23: 30000000 INFO @ Wed, 08 Dec 2021 16:51:23: 27000000 INFO @ Wed, 08 Dec 2021 16:51:24: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:51:24: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:51:24: #1 total tags in treatment: 14884579 INFO @ Wed, 08 Dec 2021 16:51:24: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:51:24: #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 16:51:24: #1 tags after filtering in treatment: 13682411 INFO @ Wed, 08 Dec 2021 16:51:24: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 16:51:24: #1 finished! INFO @ Wed, 08 Dec 2021 16:51:24: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:51:24: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:51:25: #2 number of paired peaks: 326 WARNING @ Wed, 08 Dec 2021 16:51:25: 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 16:51:25: start model_add_line... INFO @ Wed, 08 Dec 2021 16:51:25: start X-correlation... INFO @ Wed, 08 Dec 2021 16:51:25: end of X-cor INFO @ Wed, 08 Dec 2021 16:51:25: #2 finished! INFO @ Wed, 08 Dec 2021 16:51:25: #2 predicted fragment length is 140 bps INFO @ Wed, 08 Dec 2021 16:51:25: #2 alternative fragment length(s) may be 4,122,140 bps INFO @ Wed, 08 Dec 2021 16:51:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.05_model.r INFO @ Wed, 08 Dec 2021 16:51:25: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:51:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:51:28: 28000000 INFO @ Wed, 08 Dec 2021 16:51:29: 31000000 INFO @ Wed, 08 Dec 2021 16:51:34: 29000000 INFO @ Wed, 08 Dec 2021 16:51:35: 32000000 INFO @ Wed, 08 Dec 2021 16:51:39: 30000000 INFO @ Wed, 08 Dec 2021 16:51:41: 33000000 INFO @ Wed, 08 Dec 2021 16:51:44: 31000000 INFO @ Wed, 08 Dec 2021 16:51:47: 34000000 INFO @ Wed, 08 Dec 2021 16:51:50: 32000000 INFO @ Wed, 08 Dec 2021 16:51:51: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:51:52: 35000000 INFO @ Wed, 08 Dec 2021 16:51:55: 33000000 INFO @ Wed, 08 Dec 2021 16:51:58: 36000000 INFO @ Wed, 08 Dec 2021 16:52:00: 34000000 INFO @ Wed, 08 Dec 2021 16:52:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.05_peaks.xls INFO @ Wed, 08 Dec 2021 16:52:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:52:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.05_summits.bed INFO @ Wed, 08 Dec 2021 16:52:04: Done! INFO @ Wed, 08 Dec 2021 16:52:04: 37000000 pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3037 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:52:06: 35000000 INFO @ Wed, 08 Dec 2021 16:52:10: 38000000 INFO @ Wed, 08 Dec 2021 16:52:11: 36000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 16:52:16: 39000000 INFO @ Wed, 08 Dec 2021 16:52:16: 37000000 INFO @ Wed, 08 Dec 2021 16:52:18: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:52:18: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:52:18: #1 total tags in treatment: 14884579 INFO @ Wed, 08 Dec 2021 16:52:18: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:52:18: #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 16:52:18: #1 tags after filtering in treatment: 13682411 INFO @ Wed, 08 Dec 2021 16:52:18: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 16:52:18: #1 finished! INFO @ Wed, 08 Dec 2021 16:52:18: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:52:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:52:19: #2 number of paired peaks: 326 WARNING @ Wed, 08 Dec 2021 16:52:19: 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 16:52:19: start model_add_line... INFO @ Wed, 08 Dec 2021 16:52:19: start X-correlation... INFO @ Wed, 08 Dec 2021 16:52:19: end of X-cor INFO @ Wed, 08 Dec 2021 16:52:19: #2 finished! INFO @ Wed, 08 Dec 2021 16:52:19: #2 predicted fragment length is 140 bps INFO @ Wed, 08 Dec 2021 16:52:19: #2 alternative fragment length(s) may be 4,122,140 bps INFO @ Wed, 08 Dec 2021 16:52:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.10_model.r INFO @ Wed, 08 Dec 2021 16:52:19: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:52:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:52:21: 38000000 INFO @ Wed, 08 Dec 2021 16:52:26: 39000000 INFO @ Wed, 08 Dec 2021 16:52:28: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 16:52:28: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 16:52:28: #1 total tags in treatment: 14884579 INFO @ Wed, 08 Dec 2021 16:52:28: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 16:52:28: #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 16:52:28: #1 tags after filtering in treatment: 13682411 INFO @ Wed, 08 Dec 2021 16:52:28: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 16:52:28: #1 finished! INFO @ Wed, 08 Dec 2021 16:52:28: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 16:52:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 16:52:29: #2 number of paired peaks: 326 WARNING @ Wed, 08 Dec 2021 16:52:29: 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 16:52:29: start model_add_line... INFO @ Wed, 08 Dec 2021 16:52:29: start X-correlation... INFO @ Wed, 08 Dec 2021 16:52:29: end of X-cor INFO @ Wed, 08 Dec 2021 16:52:29: #2 finished! INFO @ Wed, 08 Dec 2021 16:52:29: #2 predicted fragment length is 140 bps INFO @ Wed, 08 Dec 2021 16:52:29: #2 alternative fragment length(s) may be 4,122,140 bps INFO @ Wed, 08 Dec 2021 16:52:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.20_model.r INFO @ Wed, 08 Dec 2021 16:52:29: #3 Call peaks... INFO @ Wed, 08 Dec 2021 16:52:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 16:52:46: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:52:56: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 16:52:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.10_peaks.xls INFO @ Wed, 08 Dec 2021 16:52:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:52:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.10_summits.bed INFO @ Wed, 08 Dec 2021 16:52:58: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (785 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 16:53:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.20_peaks.xls INFO @ Wed, 08 Dec 2021 16:53:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 16:53:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10342599/SRX10342599.20_summits.bed INFO @ Wed, 08 Dec 2021 16:53:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (226 records, 4 fields): 1 millis CompletedMACS2peakCalling