Job ID = 12264745 SRX = SRX2332998 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 22946693 spots for SRR5000678/SRR5000678.sra Written 22946693 spots for SRR5000678/SRR5000678.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265424 ("srTce11") has been submitted Time loading reference: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:38:43 22946693 reads; of these: 22946693 (100.00%) were paired; of these: 10165780 (44.30%) aligned concordantly 0 times 10353492 (45.12%) aligned concordantly exactly 1 time 2427421 (10.58%) aligned concordantly >1 times ---- 10165780 pairs aligned concordantly 0 times; of these: 3601649 (35.43%) aligned discordantly 1 time ---- 6564131 pairs aligned 0 times concordantly or discordantly; of these: 13128262 mates make up the pairs; of these: 11307449 (86.13%) aligned 0 times 664290 (5.06%) aligned exactly 1 time 1156523 (8.81%) aligned >1 times 75.36% overall alignment rate Time searching: 00:38:44 Overall time: 00:38:44 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 16 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] 3863048 / 16299007 = 0.2370 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/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:50:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.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 @ Sat, 03 Apr 2021 06:50:31: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:50:31: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:50:38: 1000000 INFO @ Sat, 03 Apr 2021 06:50:44: 2000000 INFO @ Sat, 03 Apr 2021 06:50:50: 3000000 INFO @ Sat, 03 Apr 2021 06:50:57: 4000000 WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:51:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.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 @ Sat, 03 Apr 2021 06:51:00: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:51:00: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:51:03: 5000000 INFO @ Sat, 03 Apr 2021 06:51:07: 1000000 INFO @ Sat, 03 Apr 2021 06:51:10: 6000000 INFO @ Sat, 03 Apr 2021 06:51:13: 2000000 INFO @ Sat, 03 Apr 2021 06:51:16: 7000000 INFO @ Sat, 03 Apr 2021 06:51:20: 3000000 INFO @ Sat, 03 Apr 2021 06:51:23: 8000000 INFO @ Sat, 03 Apr 2021 06:51:27: 4000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.7.1/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Sat, 03 Apr 2021 06:51:29: 9000000 INFO @ Sat, 03 Apr 2021 06:51:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.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 @ Sat, 03 Apr 2021 06:51:30: #1 read tag files... INFO @ Sat, 03 Apr 2021 06:51:30: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 06:51:34: 5000000 INFO @ Sat, 03 Apr 2021 06:51:36: 10000000 INFO @ Sat, 03 Apr 2021 06:51:37: 1000000 INFO @ Sat, 03 Apr 2021 06:51:41: 6000000 INFO @ Sat, 03 Apr 2021 06:51:43: 11000000 INFO @ Sat, 03 Apr 2021 06:51:45: 2000000 INFO @ Sat, 03 Apr 2021 06:51:48: 7000000 INFO @ Sat, 03 Apr 2021 06:51:49: 12000000 INFO @ Sat, 03 Apr 2021 06:51:52: 3000000 INFO @ Sat, 03 Apr 2021 06:51:55: 8000000 INFO @ Sat, 03 Apr 2021 06:51:56: 13000000 INFO @ Sat, 03 Apr 2021 06:51:59: 4000000 INFO @ Sat, 03 Apr 2021 06:52:02: 14000000 INFO @ Sat, 03 Apr 2021 06:52:03: 9000000 INFO @ Sat, 03 Apr 2021 06:52:06: 5000000 INFO @ Sat, 03 Apr 2021 06:52:09: 15000000 INFO @ Sat, 03 Apr 2021 06:52:10: 10000000 INFO @ Sat, 03 Apr 2021 06:52:14: 6000000 INFO @ Sat, 03 Apr 2021 06:52:15: 16000000 INFO @ Sat, 03 Apr 2021 06:52:17: 11000000 INFO @ Sat, 03 Apr 2021 06:52:21: 7000000 INFO @ Sat, 03 Apr 2021 06:52:22: 17000000 INFO @ Sat, 03 Apr 2021 06:52:25: 12000000 INFO @ Sat, 03 Apr 2021 06:52:28: 8000000 INFO @ Sat, 03 Apr 2021 06:52:28: 18000000 INFO @ Sat, 03 Apr 2021 06:52:32: 13000000 INFO @ Sat, 03 Apr 2021 06:52:35: 19000000 INFO @ Sat, 03 Apr 2021 06:52:36: 9000000 INFO @ Sat, 03 Apr 2021 06:52:39: 14000000 INFO @ Sat, 03 Apr 2021 06:52:41: 20000000 INFO @ Sat, 03 Apr 2021 06:52:43: 10000000 INFO @ Sat, 03 Apr 2021 06:52:47: 15000000 INFO @ Sat, 03 Apr 2021 06:52:48: 21000000 INFO @ Sat, 03 Apr 2021 06:52:50: 11000000 INFO @ Sat, 03 Apr 2021 06:52:54: 16000000 INFO @ Sat, 03 Apr 2021 06:52:54: 22000000 INFO @ Sat, 03 Apr 2021 06:52:57: 12000000 INFO @ Sat, 03 Apr 2021 06:53:01: 17000000 INFO @ Sat, 03 Apr 2021 06:53:01: 23000000 INFO @ Sat, 03 Apr 2021 06:53:05: 13000000 INFO @ Sat, 03 Apr 2021 06:53:08: 24000000 INFO @ Sat, 03 Apr 2021 06:53:08: 18000000 INFO @ Sat, 03 Apr 2021 06:53:12: 14000000 INFO @ Sat, 03 Apr 2021 06:53:14: 25000000 INFO @ Sat, 03 Apr 2021 06:53:15: 19000000 INFO @ Sat, 03 Apr 2021 06:53:19: 15000000 INFO @ Sat, 03 Apr 2021 06:53:21: 26000000 INFO @ Sat, 03 Apr 2021 06:53:22: 20000000 INFO @ Sat, 03 Apr 2021 06:53:26: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:53:26: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:53:26: #1 total tags in treatment: 9451274 INFO @ Sat, 03 Apr 2021 06:53:26: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:53:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:53:26: #1 tags after filtering in treatment: 6412753 INFO @ Sat, 03 Apr 2021 06:53:26: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 03 Apr 2021 06:53:26: #1 finished! INFO @ Sat, 03 Apr 2021 06:53:26: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:53:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:53:26: 16000000 INFO @ Sat, 03 Apr 2021 06:53:27: #2 number of paired peaks: 368 WARNING @ Sat, 03 Apr 2021 06:53:27: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Sat, 03 Apr 2021 06:53:27: start model_add_line... INFO @ Sat, 03 Apr 2021 06:53:27: start X-correlation... INFO @ Sat, 03 Apr 2021 06:53:27: end of X-cor INFO @ Sat, 03 Apr 2021 06:53:27: #2 finished! INFO @ Sat, 03 Apr 2021 06:53:27: #2 predicted fragment length is 142 bps INFO @ Sat, 03 Apr 2021 06:53:27: #2 alternative fragment length(s) may be 142,158 bps INFO @ Sat, 03 Apr 2021 06:53:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.05_model.r WARNING @ Sat, 03 Apr 2021 06:53:27: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:53:27: #2 You may need to consider one of the other alternative d(s): 142,158 WARNING @ Sat, 03 Apr 2021 06:53:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:53:27: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:53:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:53:29: 21000000 INFO @ Sat, 03 Apr 2021 06:53:34: 17000000 INFO @ Sat, 03 Apr 2021 06:53:36: 22000000 INFO @ Sat, 03 Apr 2021 06:53:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:53:41: 18000000 INFO @ Sat, 03 Apr 2021 06:53:43: 23000000 INFO @ Sat, 03 Apr 2021 06:53:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.05_peaks.xls INFO @ Sat, 03 Apr 2021 06:53:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:53:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.05_summits.bed INFO @ Sat, 03 Apr 2021 06:53:46: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2177 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:53:48: 19000000 INFO @ Sat, 03 Apr 2021 06:53:50: 24000000 INFO @ Sat, 03 Apr 2021 06:53:55: 20000000 INFO @ Sat, 03 Apr 2021 06:53:58: 25000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 06:54:02: 21000000 INFO @ Sat, 03 Apr 2021 06:54:05: 26000000 INFO @ Sat, 03 Apr 2021 06:54:09: 22000000 INFO @ Sat, 03 Apr 2021 06:54:10: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:54:10: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:54:10: #1 total tags in treatment: 9451274 INFO @ Sat, 03 Apr 2021 06:54:10: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:54:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:54:11: #1 tags after filtering in treatment: 6412753 INFO @ Sat, 03 Apr 2021 06:54:11: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 03 Apr 2021 06:54:11: #1 finished! INFO @ Sat, 03 Apr 2021 06:54:11: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:54:11: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:54:11: #2 number of paired peaks: 368 WARNING @ Sat, 03 Apr 2021 06:54:11: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Sat, 03 Apr 2021 06:54:11: start model_add_line... INFO @ Sat, 03 Apr 2021 06:54:11: start X-correlation... INFO @ Sat, 03 Apr 2021 06:54:11: end of X-cor INFO @ Sat, 03 Apr 2021 06:54:11: #2 finished! INFO @ Sat, 03 Apr 2021 06:54:11: #2 predicted fragment length is 142 bps INFO @ Sat, 03 Apr 2021 06:54:11: #2 alternative fragment length(s) may be 142,158 bps INFO @ Sat, 03 Apr 2021 06:54:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.10_model.r WARNING @ Sat, 03 Apr 2021 06:54:11: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:54:11: #2 You may need to consider one of the other alternative d(s): 142,158 WARNING @ Sat, 03 Apr 2021 06:54:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:54:11: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:54:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 06:54:15: 23000000 INFO @ Sat, 03 Apr 2021 06:54:22: 24000000 INFO @ Sat, 03 Apr 2021 06:54:24: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:54:28: 25000000 INFO @ Sat, 03 Apr 2021 06:54:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.10_peaks.xls INFO @ Sat, 03 Apr 2021 06:54:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:54:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.10_summits.bed INFO @ Sat, 03 Apr 2021 06:54:31: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (870 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 06:54:35: 26000000 INFO @ Sat, 03 Apr 2021 06:54:40: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 06:54:40: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 06:54:40: #1 total tags in treatment: 9451274 INFO @ Sat, 03 Apr 2021 06:54:40: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 06:54:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Apr 2021 06:54:40: #1 tags after filtering in treatment: 6412753 INFO @ Sat, 03 Apr 2021 06:54:40: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 03 Apr 2021 06:54:40: #1 finished! INFO @ Sat, 03 Apr 2021 06:54:40: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 06:54:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 06:54:41: #2 number of paired peaks: 368 WARNING @ Sat, 03 Apr 2021 06:54:41: Fewer paired peaks (368) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 368 pairs to build model! INFO @ Sat, 03 Apr 2021 06:54:41: start model_add_line... INFO @ Sat, 03 Apr 2021 06:54:41: start X-correlation... INFO @ Sat, 03 Apr 2021 06:54:41: end of X-cor INFO @ Sat, 03 Apr 2021 06:54:41: #2 finished! INFO @ Sat, 03 Apr 2021 06:54:41: #2 predicted fragment length is 142 bps INFO @ Sat, 03 Apr 2021 06:54:41: #2 alternative fragment length(s) may be 142,158 bps INFO @ Sat, 03 Apr 2021 06:54:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.20_model.r WARNING @ Sat, 03 Apr 2021 06:54:41: #2 Since the d (142) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 06:54:41: #2 You may need to consider one of the other alternative d(s): 142,158 WARNING @ Sat, 03 Apr 2021 06:54:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Apr 2021 06:54:41: #3 Call peaks... INFO @ Sat, 03 Apr 2021 06:54:41: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 06:54:53: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 06:55:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.20_peaks.xls INFO @ Sat, 03 Apr 2021 06:55:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 06:55:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2332998/SRX2332998.20_summits.bed INFO @ Sat, 03 Apr 2021 06:55:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (247 records, 4 fields): 2 millis CompletedMACS2peakCalling