Job ID = 12265424 SRX = SRX2332998 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: 00:41:47 22946693 reads; of these: 22946693 (100.00%) were paired; of these: 10165711 (44.30%) aligned concordantly 0 times 10353516 (45.12%) aligned concordantly exactly 1 time 2427466 (10.58%) aligned concordantly >1 times ---- 10165711 pairs aligned concordantly 0 times; of these: 3601943 (35.43%) aligned discordantly 1 time ---- 6563768 pairs aligned 0 times concordantly or discordantly; of these: 13127536 mates make up the pairs; of these: 11306689 (86.13%) aligned 0 times 664312 (5.06%) aligned exactly 1 time 1156535 (8.81%) aligned >1 times 75.36% overall alignment rate Time searching: 00:41:47 Overall time: 00:41:47 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] 3863029 / 16299367 = 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 07:57:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2332998/SRX2332998.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2332998/SRX2332998.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2332998/SRX2332998.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 07:57:40: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:57:40: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:57:48: 1000000 INFO @ Sat, 03 Apr 2021 07:57:57: 2000000 INFO @ Sat, 03 Apr 2021 07:58:06: 3000000 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 07:58:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2332998/SRX2332998.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2332998/SRX2332998.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2332998/SRX2332998.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 07:58:09: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:58:09: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:58:15: 4000000 INFO @ Sat, 03 Apr 2021 07:58:19: 1000000 INFO @ Sat, 03 Apr 2021 07:58:24: 5000000 INFO @ Sat, 03 Apr 2021 07:58:28: 2000000 INFO @ Sat, 03 Apr 2021 07:58:33: 6000000 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 07:58:38: 3000000 INFO @ Sat, 03 Apr 2021 07:58:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX2332998/SRX2332998.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX2332998/SRX2332998.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX2332998/SRX2332998.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/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 07:58:39: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:58:39: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:58:42: 7000000 INFO @ Sat, 03 Apr 2021 07:58:48: 4000000 INFO @ Sat, 03 Apr 2021 07:58:50: 1000000 INFO @ Sat, 03 Apr 2021 07:58:52: 8000000 INFO @ Sat, 03 Apr 2021 07:58:57: 5000000 INFO @ Sat, 03 Apr 2021 07:58:59: 2000000 INFO @ Sat, 03 Apr 2021 07:59:02: 9000000 INFO @ Sat, 03 Apr 2021 07:59:07: 6000000 INFO @ Sat, 03 Apr 2021 07:59:09: 3000000 INFO @ Sat, 03 Apr 2021 07:59:11: 10000000 INFO @ Sat, 03 Apr 2021 07:59:17: 7000000 INFO @ Sat, 03 Apr 2021 07:59:18: 4000000 INFO @ Sat, 03 Apr 2021 07:59:21: 11000000 INFO @ Sat, 03 Apr 2021 07:59:27: 8000000 INFO @ Sat, 03 Apr 2021 07:59:28: 5000000 INFO @ Sat, 03 Apr 2021 07:59:31: 12000000 INFO @ Sat, 03 Apr 2021 07:59:36: 9000000 INFO @ Sat, 03 Apr 2021 07:59:37: 6000000 INFO @ Sat, 03 Apr 2021 07:59:41: 13000000 INFO @ Sat, 03 Apr 2021 07:59:45: 10000000 INFO @ Sat, 03 Apr 2021 07:59:46: 7000000 INFO @ Sat, 03 Apr 2021 07:59:51: 14000000 INFO @ Sat, 03 Apr 2021 07:59:54: 11000000 INFO @ Sat, 03 Apr 2021 07:59:55: 8000000 INFO @ Sat, 03 Apr 2021 08:00:00: 15000000 INFO @ Sat, 03 Apr 2021 08:00:03: 12000000 INFO @ Sat, 03 Apr 2021 08:00:05: 9000000 INFO @ Sat, 03 Apr 2021 08:00:09: 16000000 INFO @ Sat, 03 Apr 2021 08:00:13: 13000000 INFO @ Sat, 03 Apr 2021 08:00:14: 10000000 INFO @ Sat, 03 Apr 2021 08:00:18: 17000000 INFO @ Sat, 03 Apr 2021 08:00:22: 14000000 INFO @ Sat, 03 Apr 2021 08:00:23: 11000000 INFO @ Sat, 03 Apr 2021 08:00:28: 18000000 INFO @ Sat, 03 Apr 2021 08:00:32: 15000000 INFO @ Sat, 03 Apr 2021 08:00:33: 12000000 INFO @ Sat, 03 Apr 2021 08:00:37: 19000000 INFO @ Sat, 03 Apr 2021 08:00:41: 16000000 INFO @ Sat, 03 Apr 2021 08:00:43: 13000000 INFO @ Sat, 03 Apr 2021 08:00:47: 20000000 INFO @ Sat, 03 Apr 2021 08:00:51: 17000000 INFO @ Sat, 03 Apr 2021 08:00:53: 14000000 INFO @ Sat, 03 Apr 2021 08:00:56: 21000000 INFO @ Sat, 03 Apr 2021 08:01:00: 18000000 INFO @ Sat, 03 Apr 2021 08:01:04: 15000000 INFO @ Sat, 03 Apr 2021 08:01:06: 22000000 INFO @ Sat, 03 Apr 2021 08:01:09: 19000000 INFO @ Sat, 03 Apr 2021 08:01:13: 16000000 INFO @ Sat, 03 Apr 2021 08:01:15: 23000000 INFO @ Sat, 03 Apr 2021 08:01:19: 20000000 INFO @ Sat, 03 Apr 2021 08:01:23: 17000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 08:01:25: 24000000 INFO @ Sat, 03 Apr 2021 08:01:28: 21000000 INFO @ Sat, 03 Apr 2021 08:01:32: 18000000 INFO @ Sat, 03 Apr 2021 08:01:35: 25000000 INFO @ Sat, 03 Apr 2021 08:01:38: 22000000 INFO @ Sat, 03 Apr 2021 08:01:41: 19000000 INFO @ Sat, 03 Apr 2021 08:01:44: 26000000 INFO @ Sat, 03 Apr 2021 08:01:48: 23000000 INFO @ Sat, 03 Apr 2021 08:01:51: 20000000 INFO @ Sat, 03 Apr 2021 08:01:52: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 08:01:52: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 08:01:52: #1 total tags in treatment: 9451396 INFO @ Sat, 03 Apr 2021 08:01:52: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:01:52: #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 08:01:52: #1 tags after filtering in treatment: 6412816 INFO @ Sat, 03 Apr 2021 08:01:52: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 03 Apr 2021 08:01:52: #1 finished! INFO @ Sat, 03 Apr 2021 08:01:52: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:01:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:01:53: #2 number of paired peaks: 369 WARNING @ Sat, 03 Apr 2021 08:01:53: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Sat, 03 Apr 2021 08:01:53: start model_add_line... INFO @ Sat, 03 Apr 2021 08:01:53: start X-correlation... INFO @ Sat, 03 Apr 2021 08:01:53: end of X-cor INFO @ Sat, 03 Apr 2021 08:01:53: #2 finished! INFO @ Sat, 03 Apr 2021 08:01:53: #2 predicted fragment length is 142 bps INFO @ Sat, 03 Apr 2021 08:01:53: #2 alternative fragment length(s) may be 142,157 bps INFO @ Sat, 03 Apr 2021 08:01:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2332998/SRX2332998.05_model.r WARNING @ Sat, 03 Apr 2021 08:01:53: #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 08:01:53: #2 You may need to consider one of the other alternative d(s): 142,157 WARNING @ Sat, 03 Apr 2021 08:01:53: #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 08:01:53: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:01:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:01:57: 24000000 INFO @ Sat, 03 Apr 2021 08:02:00: 21000000 INFO @ Sat, 03 Apr 2021 08:02:07: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:02:07: 25000000 INFO @ Sat, 03 Apr 2021 08:02:10: 22000000 BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 08:02:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2332998/SRX2332998.05_peaks.xls INFO @ Sat, 03 Apr 2021 08:02:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2332998/SRX2332998.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:02:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2332998/SRX2332998.05_summits.bed INFO @ Sat, 03 Apr 2021 08:02:15: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2176 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:02:17: 26000000 INFO @ Sat, 03 Apr 2021 08:02:19: 23000000 INFO @ Sat, 03 Apr 2021 08:02:24: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 08:02:24: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 08:02:24: #1 total tags in treatment: 9451396 INFO @ Sat, 03 Apr 2021 08:02:24: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:02:24: #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 08:02:25: #1 tags after filtering in treatment: 6412816 INFO @ Sat, 03 Apr 2021 08:02:25: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 03 Apr 2021 08:02:25: #1 finished! INFO @ Sat, 03 Apr 2021 08:02:25: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:02:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:02:25: #2 number of paired peaks: 369 WARNING @ Sat, 03 Apr 2021 08:02:25: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Sat, 03 Apr 2021 08:02:25: start model_add_line... INFO @ Sat, 03 Apr 2021 08:02:25: start X-correlation... INFO @ Sat, 03 Apr 2021 08:02:25: end of X-cor INFO @ Sat, 03 Apr 2021 08:02:25: #2 finished! INFO @ Sat, 03 Apr 2021 08:02:25: #2 predicted fragment length is 142 bps INFO @ Sat, 03 Apr 2021 08:02:25: #2 alternative fragment length(s) may be 142,157 bps INFO @ Sat, 03 Apr 2021 08:02:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2332998/SRX2332998.10_model.r WARNING @ Sat, 03 Apr 2021 08:02:25: #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 08:02:25: #2 You may need to consider one of the other alternative d(s): 142,157 WARNING @ Sat, 03 Apr 2021 08:02:25: #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 08:02:25: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:02:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:02:28: 24000000 INFO @ Sat, 03 Apr 2021 08:02:37: 25000000 INFO @ Sat, 03 Apr 2021 08:02:39: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:02:46: 26000000 INFO @ Sat, 03 Apr 2021 08:02:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2332998/SRX2332998.10_peaks.xls INFO @ Sat, 03 Apr 2021 08:02:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2332998/SRX2332998.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:02:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2332998/SRX2332998.10_summits.bed INFO @ Sat, 03 Apr 2021 08:02:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (871 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 08:02:53: #1 tag size is determined as 101 bps INFO @ Sat, 03 Apr 2021 08:02:53: #1 tag size = 101 INFO @ Sat, 03 Apr 2021 08:02:53: #1 total tags in treatment: 9451396 INFO @ Sat, 03 Apr 2021 08:02:53: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 08:02:53: #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 08:02:53: #1 tags after filtering in treatment: 6412816 INFO @ Sat, 03 Apr 2021 08:02:53: #1 Redundant rate of treatment: 0.32 INFO @ Sat, 03 Apr 2021 08:02:53: #1 finished! INFO @ Sat, 03 Apr 2021 08:02:53: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 08:02:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 08:02:54: #2 number of paired peaks: 369 WARNING @ Sat, 03 Apr 2021 08:02:54: Fewer paired peaks (369) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 369 pairs to build model! INFO @ Sat, 03 Apr 2021 08:02:54: start model_add_line... INFO @ Sat, 03 Apr 2021 08:02:54: start X-correlation... INFO @ Sat, 03 Apr 2021 08:02:54: end of X-cor INFO @ Sat, 03 Apr 2021 08:02:54: #2 finished! INFO @ Sat, 03 Apr 2021 08:02:54: #2 predicted fragment length is 142 bps INFO @ Sat, 03 Apr 2021 08:02:54: #2 alternative fragment length(s) may be 142,157 bps INFO @ Sat, 03 Apr 2021 08:02:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX2332998/SRX2332998.20_model.r WARNING @ Sat, 03 Apr 2021 08:02:54: #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 08:02:54: #2 You may need to consider one of the other alternative d(s): 142,157 WARNING @ Sat, 03 Apr 2021 08:02:54: #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 08:02:54: #3 Call peaks... INFO @ Sat, 03 Apr 2021 08:02:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 08:03:07: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 08:03:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX2332998/SRX2332998.20_peaks.xls INFO @ Sat, 03 Apr 2021 08:03:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX2332998/SRX2332998.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 08:03:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX2332998/SRX2332998.20_summits.bed INFO @ Sat, 03 Apr 2021 08:03:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (247 records, 4 fields): 2 millis CompletedMACS2peakCalling