Job ID = 14160323 SRX = SRX9555449 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 21932842 spots for SRR13111100/SRR13111100.sra Written 21932842 spots for SRR13111100/SRR13111100.sra fastq に変換しました。 bowtie でマッピング中... Your job 14160465 ("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: 00:17:41 21932842 reads; of these: 21932842 (100.00%) were paired; of these: 1467279 (6.69%) aligned concordantly 0 times 17771648 (81.03%) aligned concordantly exactly 1 time 2693915 (12.28%) aligned concordantly >1 times ---- 1467279 pairs aligned concordantly 0 times; of these: 725595 (49.45%) aligned discordantly 1 time ---- 741684 pairs aligned 0 times concordantly or discordantly; of these: 1483368 mates make up the pairs; of these: 852227 (57.45%) aligned 0 times 399698 (26.95%) aligned exactly 1 time 231443 (15.60%) aligned >1 times 98.06% overall alignment rate Time searching: 00:17:41 Overall time: 00:17:41 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 20 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] 1447275 / 21152072 = 0.0684 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 @ Thu, 09 Dec 2021 01:53:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.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 @ Thu, 09 Dec 2021 01:53:03: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:53:03: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:53:08: 1000000 INFO @ Thu, 09 Dec 2021 01:53:13: 2000000 INFO @ Thu, 09 Dec 2021 01:53:19: 3000000 INFO @ Thu, 09 Dec 2021 01:53:24: 4000000 INFO @ Thu, 09 Dec 2021 01:53:29: 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 @ Thu, 09 Dec 2021 01:53:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.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 @ Thu, 09 Dec 2021 01:53:33: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:53:33: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:53:35: 6000000 INFO @ Thu, 09 Dec 2021 01:53:40: 1000000 INFO @ Thu, 09 Dec 2021 01:53:42: 7000000 INFO @ Thu, 09 Dec 2021 01:53:48: 2000000 INFO @ Thu, 09 Dec 2021 01:53:49: 8000000 INFO @ Thu, 09 Dec 2021 01:53:56: 9000000 INFO @ Thu, 09 Dec 2021 01:53:56: 3000000 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 @ Thu, 09 Dec 2021 01:54:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.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 @ Thu, 09 Dec 2021 01:54:03: #1 read tag files... INFO @ Thu, 09 Dec 2021 01:54:03: #1 read treatment tags... INFO @ Thu, 09 Dec 2021 01:54:03: 10000000 INFO @ Thu, 09 Dec 2021 01:54:04: 4000000 INFO @ Thu, 09 Dec 2021 01:54:10: 11000000 INFO @ Thu, 09 Dec 2021 01:54:10: 1000000 INFO @ Thu, 09 Dec 2021 01:54:12: 5000000 INFO @ Thu, 09 Dec 2021 01:54:17: 12000000 INFO @ Thu, 09 Dec 2021 01:54:17: 2000000 INFO @ Thu, 09 Dec 2021 01:54:20: 6000000 INFO @ Thu, 09 Dec 2021 01:54:25: 3000000 INFO @ Thu, 09 Dec 2021 01:54:25: 13000000 INFO @ Thu, 09 Dec 2021 01:54:28: 7000000 INFO @ Thu, 09 Dec 2021 01:54:32: 4000000 INFO @ Thu, 09 Dec 2021 01:54:32: 14000000 INFO @ Thu, 09 Dec 2021 01:54:36: 8000000 INFO @ Thu, 09 Dec 2021 01:54:39: 5000000 INFO @ Thu, 09 Dec 2021 01:54:39: 15000000 INFO @ Thu, 09 Dec 2021 01:54:43: 9000000 INFO @ Thu, 09 Dec 2021 01:54:47: 16000000 INFO @ Thu, 09 Dec 2021 01:54:47: 6000000 INFO @ Thu, 09 Dec 2021 01:54:51: 10000000 INFO @ Thu, 09 Dec 2021 01:54:54: 17000000 INFO @ Thu, 09 Dec 2021 01:54:54: 7000000 INFO @ Thu, 09 Dec 2021 01:54:59: 11000000 INFO @ Thu, 09 Dec 2021 01:55:01: 18000000 INFO @ Thu, 09 Dec 2021 01:55:01: 8000000 INFO @ Thu, 09 Dec 2021 01:55:07: 12000000 INFO @ Thu, 09 Dec 2021 01:55:09: 19000000 INFO @ Thu, 09 Dec 2021 01:55:09: 9000000 INFO @ Thu, 09 Dec 2021 01:55:15: 13000000 INFO @ Thu, 09 Dec 2021 01:55:16: 10000000 INFO @ Thu, 09 Dec 2021 01:55:16: 20000000 INFO @ Thu, 09 Dec 2021 01:55:23: 14000000 INFO @ Thu, 09 Dec 2021 01:55:23: 11000000 INFO @ Thu, 09 Dec 2021 01:55:24: 21000000 INFO @ Thu, 09 Dec 2021 01:55:31: 12000000 INFO @ Thu, 09 Dec 2021 01:55:31: 22000000 INFO @ Thu, 09 Dec 2021 01:55:31: 15000000 INFO @ Thu, 09 Dec 2021 01:55:38: 13000000 INFO @ Thu, 09 Dec 2021 01:55:38: 23000000 INFO @ Thu, 09 Dec 2021 01:55:39: 16000000 INFO @ Thu, 09 Dec 2021 01:55:45: 14000000 INFO @ Thu, 09 Dec 2021 01:55:45: 24000000 INFO @ Thu, 09 Dec 2021 01:55:47: 17000000 INFO @ Thu, 09 Dec 2021 01:55:53: 15000000 INFO @ Thu, 09 Dec 2021 01:55:53: 25000000 INFO @ Thu, 09 Dec 2021 01:55:55: 18000000 INFO @ Thu, 09 Dec 2021 01:56:00: 16000000 INFO @ Thu, 09 Dec 2021 01:56:00: 26000000 INFO @ Thu, 09 Dec 2021 01:56:03: 19000000 INFO @ Thu, 09 Dec 2021 01:56:07: 17000000 INFO @ Thu, 09 Dec 2021 01:56:07: 27000000 INFO @ Thu, 09 Dec 2021 01:56:11: 20000000 INFO @ Thu, 09 Dec 2021 01:56:15: 18000000 INFO @ Thu, 09 Dec 2021 01:56:15: 28000000 INFO @ Thu, 09 Dec 2021 01:56:19: 21000000 INFO @ Thu, 09 Dec 2021 01:56:22: 19000000 INFO @ Thu, 09 Dec 2021 01:56:22: 29000000 INFO @ Thu, 09 Dec 2021 01:56:27: 22000000 INFO @ Thu, 09 Dec 2021 01:56:29: 20000000 INFO @ Thu, 09 Dec 2021 01:56:29: 30000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 09 Dec 2021 01:56:34: 23000000 INFO @ Thu, 09 Dec 2021 01:56:37: 21000000 INFO @ Thu, 09 Dec 2021 01:56:37: 31000000 INFO @ Thu, 09 Dec 2021 01:56:42: 24000000 INFO @ Thu, 09 Dec 2021 01:56:44: 22000000 INFO @ Thu, 09 Dec 2021 01:56:44: 32000000 INFO @ Thu, 09 Dec 2021 01:56:50: 25000000 INFO @ Thu, 09 Dec 2021 01:56:51: 23000000 INFO @ Thu, 09 Dec 2021 01:56:51: 33000000 INFO @ Thu, 09 Dec 2021 01:56:58: 26000000 INFO @ Thu, 09 Dec 2021 01:56:59: 24000000 INFO @ Thu, 09 Dec 2021 01:56:59: 34000000 INFO @ Thu, 09 Dec 2021 01:57:06: 25000000 INFO @ Thu, 09 Dec 2021 01:57:06: 35000000 INFO @ Thu, 09 Dec 2021 01:57:06: 27000000 INFO @ Thu, 09 Dec 2021 01:57:13: 36000000 INFO @ Thu, 09 Dec 2021 01:57:14: 26000000 INFO @ Thu, 09 Dec 2021 01:57:14: 28000000 INFO @ Thu, 09 Dec 2021 01:57:21: 37000000 INFO @ Thu, 09 Dec 2021 01:57:21: 27000000 INFO @ Thu, 09 Dec 2021 01:57:22: 29000000 INFO @ Thu, 09 Dec 2021 01:57:28: 38000000 INFO @ Thu, 09 Dec 2021 01:57:28: 28000000 INFO @ Thu, 09 Dec 2021 01:57:30: 30000000 INFO @ Thu, 09 Dec 2021 01:57:36: 39000000 INFO @ Thu, 09 Dec 2021 01:57:36: 29000000 BigWig に変換しました。 INFO @ Thu, 09 Dec 2021 01:57:38: 31000000 INFO @ Thu, 09 Dec 2021 01:57:43: 40000000 INFO @ Thu, 09 Dec 2021 01:57:43: 30000000 INFO @ Thu, 09 Dec 2021 01:57:44: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:57:44: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:57:44: #1 total tags in treatment: 19045303 INFO @ Thu, 09 Dec 2021 01:57:44: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:57:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:57:44: #1 tags after filtering in treatment: 17546495 INFO @ Thu, 09 Dec 2021 01:57:44: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 09 Dec 2021 01:57:44: #1 finished! INFO @ Thu, 09 Dec 2021 01:57:44: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:57:44: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:57:45: #2 number of paired peaks: 265 WARNING @ Thu, 09 Dec 2021 01:57:45: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Thu, 09 Dec 2021 01:57:45: start model_add_line... INFO @ Thu, 09 Dec 2021 01:57:45: start X-correlation... INFO @ Thu, 09 Dec 2021 01:57:45: end of X-cor INFO @ Thu, 09 Dec 2021 01:57:45: #2 finished! INFO @ Thu, 09 Dec 2021 01:57:45: #2 predicted fragment length is 134 bps INFO @ Thu, 09 Dec 2021 01:57:45: #2 alternative fragment length(s) may be 3,101,117,134 bps INFO @ Thu, 09 Dec 2021 01:57:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.05_model.r INFO @ Thu, 09 Dec 2021 01:57:45: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:57:45: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:57:46: 32000000 INFO @ Thu, 09 Dec 2021 01:57:50: 31000000 INFO @ Thu, 09 Dec 2021 01:57:54: 33000000 INFO @ Thu, 09 Dec 2021 01:57:57: 32000000 INFO @ Thu, 09 Dec 2021 01:58:02: 34000000 INFO @ Thu, 09 Dec 2021 01:58:05: 33000000 INFO @ Thu, 09 Dec 2021 01:58:10: 35000000 INFO @ Thu, 09 Dec 2021 01:58:12: 34000000 INFO @ Thu, 09 Dec 2021 01:58:15: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:58:18: 36000000 INFO @ Thu, 09 Dec 2021 01:58:19: 35000000 INFO @ Thu, 09 Dec 2021 01:58:26: 36000000 INFO @ Thu, 09 Dec 2021 01:58:26: 37000000 INFO @ Thu, 09 Dec 2021 01:58:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.05_peaks.xls INFO @ Thu, 09 Dec 2021 01:58:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.05_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:58:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.05_summits.bed INFO @ Thu, 09 Dec 2021 01:58:29: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (418 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:58:33: 37000000 INFO @ Thu, 09 Dec 2021 01:58:34: 38000000 INFO @ Thu, 09 Dec 2021 01:58:40: 38000000 INFO @ Thu, 09 Dec 2021 01:58:42: 39000000 INFO @ Thu, 09 Dec 2021 01:58:47: 39000000 INFO @ Thu, 09 Dec 2021 01:58:50: 40000000 INFO @ Thu, 09 Dec 2021 01:58:51: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:58:51: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:58:51: #1 total tags in treatment: 19045303 INFO @ Thu, 09 Dec 2021 01:58:51: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:58:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:58:51: #1 tags after filtering in treatment: 17546495 INFO @ Thu, 09 Dec 2021 01:58:51: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 09 Dec 2021 01:58:51: #1 finished! INFO @ Thu, 09 Dec 2021 01:58:51: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:58:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:58:52: #2 number of paired peaks: 265 WARNING @ Thu, 09 Dec 2021 01:58:52: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Thu, 09 Dec 2021 01:58:52: start model_add_line... INFO @ Thu, 09 Dec 2021 01:58:52: start X-correlation... INFO @ Thu, 09 Dec 2021 01:58:52: end of X-cor INFO @ Thu, 09 Dec 2021 01:58:52: #2 finished! INFO @ Thu, 09 Dec 2021 01:58:52: #2 predicted fragment length is 134 bps INFO @ Thu, 09 Dec 2021 01:58:52: #2 alternative fragment length(s) may be 3,101,117,134 bps INFO @ Thu, 09 Dec 2021 01:58:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.10_model.r INFO @ Thu, 09 Dec 2021 01:58:52: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:58:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:58:54: 40000000 INFO @ Thu, 09 Dec 2021 01:58:55: #1 tag size is determined as 51 bps INFO @ Thu, 09 Dec 2021 01:58:55: #1 tag size = 51 INFO @ Thu, 09 Dec 2021 01:58:55: #1 total tags in treatment: 19045303 INFO @ Thu, 09 Dec 2021 01:58:55: #1 user defined the maximum tags... INFO @ Thu, 09 Dec 2021 01:58:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 09 Dec 2021 01:58:55: #1 tags after filtering in treatment: 17546495 INFO @ Thu, 09 Dec 2021 01:58:55: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 09 Dec 2021 01:58:55: #1 finished! INFO @ Thu, 09 Dec 2021 01:58:55: #2 Build Peak Model... INFO @ Thu, 09 Dec 2021 01:58:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 09 Dec 2021 01:58:56: #2 number of paired peaks: 265 WARNING @ Thu, 09 Dec 2021 01:58:56: Fewer paired peaks (265) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 265 pairs to build model! INFO @ Thu, 09 Dec 2021 01:58:56: start model_add_line... INFO @ Thu, 09 Dec 2021 01:58:56: start X-correlation... INFO @ Thu, 09 Dec 2021 01:58:56: end of X-cor INFO @ Thu, 09 Dec 2021 01:58:56: #2 finished! INFO @ Thu, 09 Dec 2021 01:58:56: #2 predicted fragment length is 134 bps INFO @ Thu, 09 Dec 2021 01:58:56: #2 alternative fragment length(s) may be 3,101,117,134 bps INFO @ Thu, 09 Dec 2021 01:58:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.20_model.r INFO @ Thu, 09 Dec 2021 01:58:56: #3 Call peaks... INFO @ Thu, 09 Dec 2021 01:58:56: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 09 Dec 2021 01:59:22: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:59:26: #3 Call peaks for each chromosome... INFO @ Thu, 09 Dec 2021 01:59:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.10_peaks.xls INFO @ Thu, 09 Dec 2021 01:59:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.10_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:59:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.10_summits.bed INFO @ Thu, 09 Dec 2021 01:59:36: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (316 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Thu, 09 Dec 2021 01:59:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.20_peaks.xls INFO @ Thu, 09 Dec 2021 01:59:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.20_peaks.narrowPeak INFO @ Thu, 09 Dec 2021 01:59:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX9555449/SRX9555449.20_summits.bed INFO @ Thu, 09 Dec 2021 01:59:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (213 records, 4 fields): 1 millis CompletedMACS2peakCalling