Job ID = 12265367 SRX = SRX3029127 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: 00:20:39 27055709 reads; of these: 27055709 (100.00%) were paired; of these: 12347542 (45.64%) aligned concordantly 0 times 12680889 (46.87%) aligned concordantly exactly 1 time 2027278 (7.49%) aligned concordantly >1 times ---- 12347542 pairs aligned concordantly 0 times; of these: 2155286 (17.46%) aligned discordantly 1 time ---- 10192256 pairs aligned 0 times concordantly or discordantly; of these: 20384512 mates make up the pairs; of these: 19297452 (94.67%) aligned 0 times 461765 (2.27%) aligned exactly 1 time 625295 (3.07%) aligned >1 times 64.34% overall alignment rate Time searching: 00:20:39 Overall time: 00:20:39 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] 4976916 / 16689303 = 0.2982 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 07:15:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.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 07:15:20: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:15:20: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:15:27: 1000000 INFO @ Sat, 03 Apr 2021 07:15:34: 2000000 INFO @ Sat, 03 Apr 2021 07:15:40: 3000000 INFO @ Sat, 03 Apr 2021 07:15:47: 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 07:15:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.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 07:15:50: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:15:50: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:15:53: 5000000 INFO @ Sat, 03 Apr 2021 07:15:56: 1000000 INFO @ Sat, 03 Apr 2021 07:15:59: 6000000 INFO @ Sat, 03 Apr 2021 07:16:02: 2000000 INFO @ Sat, 03 Apr 2021 07:16:06: 7000000 INFO @ Sat, 03 Apr 2021 07:16:08: 3000000 INFO @ Sat, 03 Apr 2021 07:16:12: 8000000 INFO @ Sat, 03 Apr 2021 07:16:13: 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 07:16:19: 9000000 INFO @ Sat, 03 Apr 2021 07:16:19: 5000000 INFO @ Sat, 03 Apr 2021 07:16:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.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 07:16:20: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:16:20: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:16:25: 6000000 INFO @ Sat, 03 Apr 2021 07:16:25: 10000000 INFO @ Sat, 03 Apr 2021 07:16:26: 1000000 INFO @ Sat, 03 Apr 2021 07:16:30: 7000000 INFO @ Sat, 03 Apr 2021 07:16:31: 11000000 INFO @ Sat, 03 Apr 2021 07:16:31: 2000000 INFO @ Sat, 03 Apr 2021 07:16:36: 8000000 INFO @ Sat, 03 Apr 2021 07:16:37: 3000000 INFO @ Sat, 03 Apr 2021 07:16:38: 12000000 INFO @ Sat, 03 Apr 2021 07:16:41: 9000000 INFO @ Sat, 03 Apr 2021 07:16:43: 4000000 INFO @ Sat, 03 Apr 2021 07:16:44: 13000000 INFO @ Sat, 03 Apr 2021 07:16:47: 10000000 INFO @ Sat, 03 Apr 2021 07:16:48: 5000000 INFO @ Sat, 03 Apr 2021 07:16:50: 14000000 INFO @ Sat, 03 Apr 2021 07:16:52: 11000000 INFO @ Sat, 03 Apr 2021 07:16:54: 6000000 INFO @ Sat, 03 Apr 2021 07:16:57: 15000000 INFO @ Sat, 03 Apr 2021 07:16:58: 12000000 INFO @ Sat, 03 Apr 2021 07:16:59: 7000000 INFO @ Sat, 03 Apr 2021 07:17:03: 16000000 INFO @ Sat, 03 Apr 2021 07:17:04: 13000000 INFO @ Sat, 03 Apr 2021 07:17:05: 8000000 INFO @ Sat, 03 Apr 2021 07:17:09: 14000000 INFO @ Sat, 03 Apr 2021 07:17:09: 17000000 INFO @ Sat, 03 Apr 2021 07:17:11: 9000000 INFO @ Sat, 03 Apr 2021 07:17:15: 15000000 INFO @ Sat, 03 Apr 2021 07:17:16: 18000000 INFO @ Sat, 03 Apr 2021 07:17:16: 10000000 INFO @ Sat, 03 Apr 2021 07:17:21: 16000000 INFO @ Sat, 03 Apr 2021 07:17:22: 19000000 INFO @ Sat, 03 Apr 2021 07:17:22: 11000000 INFO @ Sat, 03 Apr 2021 07:17:27: 17000000 INFO @ Sat, 03 Apr 2021 07:17:27: 12000000 INFO @ Sat, 03 Apr 2021 07:17:28: 20000000 INFO @ Sat, 03 Apr 2021 07:17:32: 18000000 INFO @ Sat, 03 Apr 2021 07:17:33: 13000000 INFO @ Sat, 03 Apr 2021 07:17:34: 21000000 INFO @ Sat, 03 Apr 2021 07:17:38: 19000000 INFO @ Sat, 03 Apr 2021 07:17:38: 14000000 INFO @ Sat, 03 Apr 2021 07:17:41: 22000000 INFO @ Sat, 03 Apr 2021 07:17:43: 20000000 INFO @ Sat, 03 Apr 2021 07:17:44: 15000000 INFO @ Sat, 03 Apr 2021 07:17:47: 23000000 INFO @ Sat, 03 Apr 2021 07:17:49: 21000000 INFO @ Sat, 03 Apr 2021 07:17:50: 16000000 INFO @ Sat, 03 Apr 2021 07:17:53: 24000000 INFO @ Sat, 03 Apr 2021 07:17:55: 22000000 INFO @ Sat, 03 Apr 2021 07:17:55: 17000000 INFO @ Sat, 03 Apr 2021 07:17:59: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 07:17:59: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 07:17:59: #1 total tags in treatment: 10376976 INFO @ Sat, 03 Apr 2021 07:17:59: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:17:59: #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 07:17:59: #1 tags after filtering in treatment: 7632634 INFO @ Sat, 03 Apr 2021 07:17:59: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 07:17:59: #1 finished! INFO @ Sat, 03 Apr 2021 07:17:59: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:17:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:17:59: #2 number of paired peaks: 678 WARNING @ Sat, 03 Apr 2021 07:17:59: Fewer paired peaks (678) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 678 pairs to build model! INFO @ Sat, 03 Apr 2021 07:17:59: start model_add_line... INFO @ Sat, 03 Apr 2021 07:17:59: start X-correlation... INFO @ Sat, 03 Apr 2021 07:17:59: end of X-cor INFO @ Sat, 03 Apr 2021 07:17:59: #2 finished! INFO @ Sat, 03 Apr 2021 07:17:59: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Apr 2021 07:17:59: #2 alternative fragment length(s) may be 123 bps INFO @ Sat, 03 Apr 2021 07:17:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.05_model.r WARNING @ Sat, 03 Apr 2021 07:17:59: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:17:59: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sat, 03 Apr 2021 07:17:59: #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 07:17:59: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:17:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:18:00: 18000000 INFO @ Sat, 03 Apr 2021 07:18:00: 23000000 INFO @ Sat, 03 Apr 2021 07:18:06: 19000000 INFO @ Sat, 03 Apr 2021 07:18:06: 24000000 INFO @ Sat, 03 Apr 2021 07:18:10: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 07:18:10: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 07:18:10: #1 total tags in treatment: 10376976 INFO @ Sat, 03 Apr 2021 07:18:10: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:18:10: #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 07:18:10: #1 tags after filtering in treatment: 7632634 INFO @ Sat, 03 Apr 2021 07:18:10: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 07:18:10: #1 finished! INFO @ Sat, 03 Apr 2021 07:18:10: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:18:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:18:11: #2 number of paired peaks: 678 WARNING @ Sat, 03 Apr 2021 07:18:11: Fewer paired peaks (678) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 678 pairs to build model! INFO @ Sat, 03 Apr 2021 07:18:11: start model_add_line... INFO @ Sat, 03 Apr 2021 07:18:11: 20000000 INFO @ Sat, 03 Apr 2021 07:18:11: start X-correlation... INFO @ Sat, 03 Apr 2021 07:18:11: end of X-cor INFO @ Sat, 03 Apr 2021 07:18:11: #2 finished! INFO @ Sat, 03 Apr 2021 07:18:11: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Apr 2021 07:18:11: #2 alternative fragment length(s) may be 123 bps INFO @ Sat, 03 Apr 2021 07:18:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.10_model.r WARNING @ Sat, 03 Apr 2021 07:18:11: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:18:11: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sat, 03 Apr 2021 07:18:11: #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 07:18:11: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:18:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:18:16: 21000000 INFO @ Sat, 03 Apr 2021 07:18:18: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:18:21: 22000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:18:27: 23000000 INFO @ Sat, 03 Apr 2021 07:18:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:18:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:18:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.05_summits.bed INFO @ Sat, 03 Apr 2021 07:18:27: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5975 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:18:29: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:18:32: 24000000 INFO @ Sat, 03 Apr 2021 07:18:36: #1 tag size is determined as 76 bps INFO @ Sat, 03 Apr 2021 07:18:36: #1 tag size = 76 INFO @ Sat, 03 Apr 2021 07:18:36: #1 total tags in treatment: 10376976 INFO @ Sat, 03 Apr 2021 07:18:36: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:18:36: #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 07:18:36: #1 tags after filtering in treatment: 7632634 INFO @ Sat, 03 Apr 2021 07:18:36: #1 Redundant rate of treatment: 0.26 INFO @ Sat, 03 Apr 2021 07:18:36: #1 finished! INFO @ Sat, 03 Apr 2021 07:18:36: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:18:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:18:37: #2 number of paired peaks: 678 WARNING @ Sat, 03 Apr 2021 07:18:37: Fewer paired peaks (678) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 678 pairs to build model! INFO @ Sat, 03 Apr 2021 07:18:37: start model_add_line... INFO @ Sat, 03 Apr 2021 07:18:37: start X-correlation... INFO @ Sat, 03 Apr 2021 07:18:37: end of X-cor INFO @ Sat, 03 Apr 2021 07:18:37: #2 finished! INFO @ Sat, 03 Apr 2021 07:18:37: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Apr 2021 07:18:37: #2 alternative fragment length(s) may be 123 bps INFO @ Sat, 03 Apr 2021 07:18:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.20_model.r WARNING @ Sat, 03 Apr 2021 07:18:37: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Apr 2021 07:18:37: #2 You may need to consider one of the other alternative d(s): 123 WARNING @ Sat, 03 Apr 2021 07:18:37: #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 07:18:37: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:18:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:18:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:18:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:18:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.10_summits.bed INFO @ Sat, 03 Apr 2021 07:18:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3502 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:18:55: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:19:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:19:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:19:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX3029127/SRX3029127.20_summits.bed INFO @ Sat, 03 Apr 2021 07:19:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1599 records, 4 fields): 3 millis CompletedMACS2peakCalling