Job ID = 14158884 SRX = SRX10342592 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: 00:15:49 24536500 reads; of these: 24536500 (100.00%) were paired; of these: 9692970 (39.50%) aligned concordantly 0 times 12908119 (52.61%) aligned concordantly exactly 1 time 1935411 (7.89%) aligned concordantly >1 times ---- 9692970 pairs aligned concordantly 0 times; of these: 6036414 (62.28%) aligned discordantly 1 time ---- 3656556 pairs aligned 0 times concordantly or discordantly; of these: 7313112 mates make up the pairs; of these: 5131142 (70.16%) aligned 0 times 876264 (11.98%) aligned exactly 1 time 1305706 (17.85%) aligned >1 times 89.54% overall alignment rate Time searching: 00:15:49 Overall time: 00:15:49 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] 7422247 / 20871894 = 0.3556 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 18:35:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.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 18:35:42: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:35:42: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:35:47: 1000000 INFO @ Wed, 08 Dec 2021 18:35:52: 2000000 INFO @ Wed, 08 Dec 2021 18:35:57: 3000000 INFO @ Wed, 08 Dec 2021 18:36:01: 4000000 INFO @ Wed, 08 Dec 2021 18:36:06: 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 18:36:11: 6000000 INFO @ Wed, 08 Dec 2021 18:36:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.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 18:36:12: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:36:12: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:36:16: 7000000 INFO @ Wed, 08 Dec 2021 18:36:17: 1000000 INFO @ Wed, 08 Dec 2021 18:36:21: 8000000 INFO @ Wed, 08 Dec 2021 18:36:22: 2000000 INFO @ Wed, 08 Dec 2021 18:36:26: 9000000 INFO @ Wed, 08 Dec 2021 18:36:28: 3000000 INFO @ Wed, 08 Dec 2021 18:36:32: 10000000 INFO @ Wed, 08 Dec 2021 18:36:33: 4000000 INFO @ Wed, 08 Dec 2021 18:36:37: 11000000 INFO @ Wed, 08 Dec 2021 18:36:38: 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 18:36:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.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 18:36:42: #1 read tag files... INFO @ Wed, 08 Dec 2021 18:36:42: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 18:36:42: 12000000 INFO @ Wed, 08 Dec 2021 18:36:44: 6000000 INFO @ Wed, 08 Dec 2021 18:36:48: 1000000 INFO @ Wed, 08 Dec 2021 18:36:48: 13000000 INFO @ Wed, 08 Dec 2021 18:36:50: 7000000 INFO @ Wed, 08 Dec 2021 18:36:54: 14000000 INFO @ Wed, 08 Dec 2021 18:36:54: 2000000 INFO @ Wed, 08 Dec 2021 18:36:56: 8000000 INFO @ Wed, 08 Dec 2021 18:37:00: 15000000 INFO @ Wed, 08 Dec 2021 18:37:01: 3000000 INFO @ Wed, 08 Dec 2021 18:37:02: 9000000 INFO @ Wed, 08 Dec 2021 18:37:06: 16000000 INFO @ Wed, 08 Dec 2021 18:37:08: 4000000 INFO @ Wed, 08 Dec 2021 18:37:08: 10000000 INFO @ Wed, 08 Dec 2021 18:37:12: 17000000 INFO @ Wed, 08 Dec 2021 18:37:14: 5000000 INFO @ Wed, 08 Dec 2021 18:37:14: 11000000 INFO @ Wed, 08 Dec 2021 18:37:18: 18000000 INFO @ Wed, 08 Dec 2021 18:37:20: 12000000 INFO @ Wed, 08 Dec 2021 18:37:21: 6000000 INFO @ Wed, 08 Dec 2021 18:37:24: 19000000 INFO @ Wed, 08 Dec 2021 18:37:26: 13000000 INFO @ Wed, 08 Dec 2021 18:37:27: 7000000 INFO @ Wed, 08 Dec 2021 18:37:30: 20000000 INFO @ Wed, 08 Dec 2021 18:37:32: 14000000 INFO @ Wed, 08 Dec 2021 18:37:34: 8000000 INFO @ Wed, 08 Dec 2021 18:37:36: 21000000 INFO @ Wed, 08 Dec 2021 18:37:38: 15000000 INFO @ Wed, 08 Dec 2021 18:37:41: 9000000 INFO @ Wed, 08 Dec 2021 18:37:42: 22000000 INFO @ Wed, 08 Dec 2021 18:37:44: 16000000 INFO @ Wed, 08 Dec 2021 18:37:48: 10000000 INFO @ Wed, 08 Dec 2021 18:37:49: 23000000 INFO @ Wed, 08 Dec 2021 18:37:50: 17000000 INFO @ Wed, 08 Dec 2021 18:37:54: 11000000 INFO @ Wed, 08 Dec 2021 18:37:55: 24000000 INFO @ Wed, 08 Dec 2021 18:37:56: 18000000 INFO @ Wed, 08 Dec 2021 18:38:01: 25000000 INFO @ Wed, 08 Dec 2021 18:38:01: 12000000 INFO @ Wed, 08 Dec 2021 18:38:02: 19000000 INFO @ Wed, 08 Dec 2021 18:38:07: 26000000 INFO @ Wed, 08 Dec 2021 18:38:08: 13000000 INFO @ Wed, 08 Dec 2021 18:38:09: 20000000 INFO @ Wed, 08 Dec 2021 18:38:13: 27000000 INFO @ Wed, 08 Dec 2021 18:38:15: 21000000 INFO @ Wed, 08 Dec 2021 18:38:15: 14000000 INFO @ Wed, 08 Dec 2021 18:38:19: 28000000 INFO @ Wed, 08 Dec 2021 18:38:20: 22000000 INFO @ Wed, 08 Dec 2021 18:38:22: 15000000 INFO @ Wed, 08 Dec 2021 18:38:25: 29000000 INFO @ Wed, 08 Dec 2021 18:38:25: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:38:25: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:38:25: #1 total tags in treatment: 9162755 INFO @ Wed, 08 Dec 2021 18:38:25: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:38:25: #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 18:38:25: #1 tags after filtering in treatment: 8469705 INFO @ Wed, 08 Dec 2021 18:38:25: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 18:38:25: #1 finished! INFO @ Wed, 08 Dec 2021 18:38:25: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:38:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:38:26: #2 number of paired peaks: 573 WARNING @ Wed, 08 Dec 2021 18:38:26: Fewer paired peaks (573) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 573 pairs to build model! INFO @ Wed, 08 Dec 2021 18:38:26: start model_add_line... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 18:38:26: start X-correlation... INFO @ Wed, 08 Dec 2021 18:38:26: end of X-cor INFO @ Wed, 08 Dec 2021 18:38:26: #2 finished! INFO @ Wed, 08 Dec 2021 18:38:26: #2 predicted fragment length is 136 bps INFO @ Wed, 08 Dec 2021 18:38:26: #2 alternative fragment length(s) may be 4,136,155 bps INFO @ Wed, 08 Dec 2021 18:38:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.05_model.r INFO @ Wed, 08 Dec 2021 18:38:26: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:38:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:38:26: 23000000 INFO @ Wed, 08 Dec 2021 18:38:29: 16000000 INFO @ Wed, 08 Dec 2021 18:38:33: 24000000 INFO @ Wed, 08 Dec 2021 18:38:36: 17000000 INFO @ Wed, 08 Dec 2021 18:38:39: 25000000 INFO @ Wed, 08 Dec 2021 18:38:43: 18000000 INFO @ Wed, 08 Dec 2021 18:38:44: 26000000 INFO @ Wed, 08 Dec 2021 18:38:45: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:38:49: 19000000 INFO @ Wed, 08 Dec 2021 18:38:50: 27000000 INFO @ Wed, 08 Dec 2021 18:38:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.05_peaks.xls INFO @ Wed, 08 Dec 2021 18:38:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:38:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.05_summits.bed INFO @ Wed, 08 Dec 2021 18:38:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1828 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:38:56: 20000000 INFO @ Wed, 08 Dec 2021 18:38:56: 28000000 INFO @ Wed, 08 Dec 2021 18:39:02: 29000000 INFO @ Wed, 08 Dec 2021 18:39:03: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:39:03: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:39:03: #1 total tags in treatment: 9162755 INFO @ Wed, 08 Dec 2021 18:39:03: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:39:03: #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 18:39:03: #1 tags after filtering in treatment: 8469705 INFO @ Wed, 08 Dec 2021 18:39:03: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 18:39:03: #1 finished! INFO @ Wed, 08 Dec 2021 18:39:03: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:39:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:39:03: 21000000 INFO @ Wed, 08 Dec 2021 18:39:03: #2 number of paired peaks: 573 WARNING @ Wed, 08 Dec 2021 18:39:03: Fewer paired peaks (573) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 573 pairs to build model! INFO @ Wed, 08 Dec 2021 18:39:03: start model_add_line... INFO @ Wed, 08 Dec 2021 18:39:04: start X-correlation... INFO @ Wed, 08 Dec 2021 18:39:04: end of X-cor INFO @ Wed, 08 Dec 2021 18:39:04: #2 finished! INFO @ Wed, 08 Dec 2021 18:39:04: #2 predicted fragment length is 136 bps INFO @ Wed, 08 Dec 2021 18:39:04: #2 alternative fragment length(s) may be 4,136,155 bps INFO @ Wed, 08 Dec 2021 18:39:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.10_model.r INFO @ Wed, 08 Dec 2021 18:39:04: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:39:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:39:09: 22000000 INFO @ Wed, 08 Dec 2021 18:39:16: 23000000 BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 18:39:20: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:39:22: 24000000 INFO @ Wed, 08 Dec 2021 18:39:28: 25000000 INFO @ Wed, 08 Dec 2021 18:39:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.10_peaks.xls INFO @ Wed, 08 Dec 2021 18:39:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:39:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.10_summits.bed INFO @ Wed, 08 Dec 2021 18:39:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (486 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 18:39:34: 26000000 INFO @ Wed, 08 Dec 2021 18:39:40: 27000000 INFO @ Wed, 08 Dec 2021 18:39:47: 28000000 INFO @ Wed, 08 Dec 2021 18:39:53: 29000000 INFO @ Wed, 08 Dec 2021 18:39:53: #1 tag size is determined as 38 bps INFO @ Wed, 08 Dec 2021 18:39:53: #1 tag size = 38 INFO @ Wed, 08 Dec 2021 18:39:53: #1 total tags in treatment: 9162755 INFO @ Wed, 08 Dec 2021 18:39:53: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 18:39:53: #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 18:39:53: #1 tags after filtering in treatment: 8469705 INFO @ Wed, 08 Dec 2021 18:39:53: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 08 Dec 2021 18:39:53: #1 finished! INFO @ Wed, 08 Dec 2021 18:39:53: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 18:39:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 18:39:54: #2 number of paired peaks: 573 WARNING @ Wed, 08 Dec 2021 18:39:54: Fewer paired peaks (573) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 573 pairs to build model! INFO @ Wed, 08 Dec 2021 18:39:54: start model_add_line... INFO @ Wed, 08 Dec 2021 18:39:54: start X-correlation... INFO @ Wed, 08 Dec 2021 18:39:54: end of X-cor INFO @ Wed, 08 Dec 2021 18:39:54: #2 finished! INFO @ Wed, 08 Dec 2021 18:39:54: #2 predicted fragment length is 136 bps INFO @ Wed, 08 Dec 2021 18:39:54: #2 alternative fragment length(s) may be 4,136,155 bps INFO @ Wed, 08 Dec 2021 18:39:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.20_model.r INFO @ Wed, 08 Dec 2021 18:39:54: #3 Call peaks... INFO @ Wed, 08 Dec 2021 18:39:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 18:40:10: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 18:40:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.20_peaks.xls INFO @ Wed, 08 Dec 2021 18:40:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 18:40:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX10342592/SRX10342592.20_summits.bed INFO @ Wed, 08 Dec 2021 18:40:18: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (233 records, 4 fields): 2 millis CompletedMACS2peakCalling