Job ID = 14158025 SRX = SRX10641217 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 14718800 spots for SRR14280061/SRR14280061.sra Written 14718800 spots for SRR14280061/SRR14280061.sra fastq に変換しました。 bowtie でマッピング中... Your job 14158320 ("srTce11") has been submitted Time loading reference: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:23:49 14718800 reads; of these: 14718800 (100.00%) were paired; of these: 6764545 (45.96%) aligned concordantly 0 times 6719205 (45.65%) aligned concordantly exactly 1 time 1235050 (8.39%) aligned concordantly >1 times ---- 6764545 pairs aligned concordantly 0 times; of these: 1998334 (29.54%) aligned discordantly 1 time ---- 4766211 pairs aligned 0 times concordantly or discordantly; of these: 9532422 mates make up the pairs; of these: 8694307 (91.21%) aligned 0 times 409922 (4.30%) aligned exactly 1 time 428193 (4.49%) aligned >1 times 70.47% overall alignment rate Time searching: 00:23:50 Overall time: 00:23:50 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] 1135392 / 9915234 = 0.1145 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 14:31:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.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 14:31:52: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:31:52: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:31:59: 1000000 INFO @ Wed, 08 Dec 2021 14:32:06: 2000000 INFO @ Wed, 08 Dec 2021 14:32:12: 3000000 INFO @ Wed, 08 Dec 2021 14:32:19: 4000000 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 14:32:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.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 14:32:22: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:32:22: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:32:26: 5000000 INFO @ Wed, 08 Dec 2021 14:32:29: 1000000 INFO @ Wed, 08 Dec 2021 14:32:33: 6000000 INFO @ Wed, 08 Dec 2021 14:32:36: 2000000 INFO @ Wed, 08 Dec 2021 14:32:41: 7000000 INFO @ Wed, 08 Dec 2021 14:32:43: 3000000 INFO @ Wed, 08 Dec 2021 14:32:48: 8000000 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 14:32:51: 4000000 INFO @ Wed, 08 Dec 2021 14:32:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.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 14:32:52: #1 read tag files... INFO @ Wed, 08 Dec 2021 14:32:52: #1 read treatment tags... INFO @ Wed, 08 Dec 2021 14:32:55: 9000000 INFO @ Wed, 08 Dec 2021 14:32:58: 5000000 INFO @ Wed, 08 Dec 2021 14:32:59: 1000000 INFO @ Wed, 08 Dec 2021 14:33:03: 10000000 INFO @ Wed, 08 Dec 2021 14:33:05: 6000000 INFO @ Wed, 08 Dec 2021 14:33:07: 2000000 INFO @ Wed, 08 Dec 2021 14:33:10: 11000000 INFO @ Wed, 08 Dec 2021 14:33:12: 7000000 INFO @ Wed, 08 Dec 2021 14:33:14: 3000000 INFO @ Wed, 08 Dec 2021 14:33:18: 12000000 INFO @ Wed, 08 Dec 2021 14:33:19: 8000000 INFO @ Wed, 08 Dec 2021 14:33:21: 4000000 INFO @ Wed, 08 Dec 2021 14:33:25: 13000000 INFO @ Wed, 08 Dec 2021 14:33:26: 9000000 INFO @ Wed, 08 Dec 2021 14:33:29: 5000000 INFO @ Wed, 08 Dec 2021 14:33:32: 14000000 INFO @ Wed, 08 Dec 2021 14:33:33: 10000000 INFO @ Wed, 08 Dec 2021 14:33:36: 6000000 INFO @ Wed, 08 Dec 2021 14:33:40: 15000000 INFO @ Wed, 08 Dec 2021 14:33:41: 11000000 INFO @ Wed, 08 Dec 2021 14:33:43: 7000000 INFO @ Wed, 08 Dec 2021 14:33:47: 16000000 INFO @ Wed, 08 Dec 2021 14:33:48: 12000000 INFO @ Wed, 08 Dec 2021 14:33:50: 8000000 INFO @ Wed, 08 Dec 2021 14:33:54: 17000000 INFO @ Wed, 08 Dec 2021 14:33:55: 13000000 INFO @ Wed, 08 Dec 2021 14:33:58: 9000000 INFO @ Wed, 08 Dec 2021 14:34:02: 18000000 INFO @ Wed, 08 Dec 2021 14:34:02: 14000000 INFO @ Wed, 08 Dec 2021 14:34:05: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 14:34:05: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 14:34:05: #1 total tags in treatment: 6996777 INFO @ Wed, 08 Dec 2021 14:34:05: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:34:05: #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 14:34:05: 10000000 INFO @ Wed, 08 Dec 2021 14:34:05: #1 tags after filtering in treatment: 6535313 INFO @ Wed, 08 Dec 2021 14:34:05: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 14:34:05: #1 finished! INFO @ Wed, 08 Dec 2021 14:34:05: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:34:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:34:06: #2 number of paired peaks: 529 WARNING @ Wed, 08 Dec 2021 14:34:06: Fewer paired peaks (529) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 529 pairs to build model! INFO @ Wed, 08 Dec 2021 14:34:06: start model_add_line... INFO @ Wed, 08 Dec 2021 14:34:06: start X-correlation... INFO @ Wed, 08 Dec 2021 14:34:06: end of X-cor INFO @ Wed, 08 Dec 2021 14:34:06: #2 finished! INFO @ Wed, 08 Dec 2021 14:34:06: #2 predicted fragment length is 218 bps INFO @ Wed, 08 Dec 2021 14:34:06: #2 alternative fragment length(s) may be 218 bps INFO @ Wed, 08 Dec 2021 14:34:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.05_model.r WARNING @ Wed, 08 Dec 2021 14:34:06: #2 Since the d (218) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:34:06: #2 You may need to consider one of the other alternative d(s): 218 WARNING @ Wed, 08 Dec 2021 14:34:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:34:06: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:34:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 08 Dec 2021 14:34:09: 15000000 INFO @ Wed, 08 Dec 2021 14:34:12: 11000000 INFO @ Wed, 08 Dec 2021 14:34:16: 16000000 INFO @ Wed, 08 Dec 2021 14:34:20: 12000000 INFO @ Wed, 08 Dec 2021 14:34:21: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:34:23: 17000000 INFO @ Wed, 08 Dec 2021 14:34:27: 13000000 INFO @ Wed, 08 Dec 2021 14:34:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.05_peaks.xls INFO @ Wed, 08 Dec 2021 14:34:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.05_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:34:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.05_summits.bed INFO @ Wed, 08 Dec 2021 14:34:27: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (432 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:34:30: 18000000 INFO @ Wed, 08 Dec 2021 14:34:34: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 14:34:34: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 14:34:34: #1 total tags in treatment: 6996777 INFO @ Wed, 08 Dec 2021 14:34:34: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:34:34: #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 14:34:34: #1 tags after filtering in treatment: 6535313 INFO @ Wed, 08 Dec 2021 14:34:34: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 14:34:34: #1 finished! INFO @ Wed, 08 Dec 2021 14:34:34: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:34:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:34:34: 14000000 INFO @ Wed, 08 Dec 2021 14:34:34: #2 number of paired peaks: 529 WARNING @ Wed, 08 Dec 2021 14:34:34: Fewer paired peaks (529) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 529 pairs to build model! INFO @ Wed, 08 Dec 2021 14:34:34: start model_add_line... INFO @ Wed, 08 Dec 2021 14:34:34: start X-correlation... INFO @ Wed, 08 Dec 2021 14:34:34: end of X-cor INFO @ Wed, 08 Dec 2021 14:34:34: #2 finished! INFO @ Wed, 08 Dec 2021 14:34:34: #2 predicted fragment length is 218 bps INFO @ Wed, 08 Dec 2021 14:34:34: #2 alternative fragment length(s) may be 218 bps INFO @ Wed, 08 Dec 2021 14:34:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.10_model.r WARNING @ Wed, 08 Dec 2021 14:34:34: #2 Since the d (218) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:34:34: #2 You may need to consider one of the other alternative d(s): 218 WARNING @ Wed, 08 Dec 2021 14:34:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:34:34: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:34:34: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 08 Dec 2021 14:34:41: 15000000 INFO @ Wed, 08 Dec 2021 14:34:48: 16000000 INFO @ Wed, 08 Dec 2021 14:34:49: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:34:55: 17000000 INFO @ Wed, 08 Dec 2021 14:34:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.10_peaks.xls INFO @ Wed, 08 Dec 2021 14:34:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.10_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:34:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.10_summits.bed INFO @ Wed, 08 Dec 2021 14:34:56: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (330 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 08 Dec 2021 14:35:02: 18000000 INFO @ Wed, 08 Dec 2021 14:35:05: #1 tag size is determined as 150 bps INFO @ Wed, 08 Dec 2021 14:35:05: #1 tag size = 150 INFO @ Wed, 08 Dec 2021 14:35:05: #1 total tags in treatment: 6996777 INFO @ Wed, 08 Dec 2021 14:35:05: #1 user defined the maximum tags... INFO @ Wed, 08 Dec 2021 14:35:05: #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 14:35:05: #1 tags after filtering in treatment: 6535313 INFO @ Wed, 08 Dec 2021 14:35:05: #1 Redundant rate of treatment: 0.07 INFO @ Wed, 08 Dec 2021 14:35:05: #1 finished! INFO @ Wed, 08 Dec 2021 14:35:05: #2 Build Peak Model... INFO @ Wed, 08 Dec 2021 14:35:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 08 Dec 2021 14:35:05: #2 number of paired peaks: 529 WARNING @ Wed, 08 Dec 2021 14:35:05: Fewer paired peaks (529) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 529 pairs to build model! INFO @ Wed, 08 Dec 2021 14:35:05: start model_add_line... INFO @ Wed, 08 Dec 2021 14:35:06: start X-correlation... INFO @ Wed, 08 Dec 2021 14:35:06: end of X-cor INFO @ Wed, 08 Dec 2021 14:35:06: #2 finished! INFO @ Wed, 08 Dec 2021 14:35:06: #2 predicted fragment length is 218 bps INFO @ Wed, 08 Dec 2021 14:35:06: #2 alternative fragment length(s) may be 218 bps INFO @ Wed, 08 Dec 2021 14:35:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.20_model.r WARNING @ Wed, 08 Dec 2021 14:35:06: #2 Since the d (218) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 08 Dec 2021 14:35:06: #2 You may need to consider one of the other alternative d(s): 218 WARNING @ Wed, 08 Dec 2021 14:35:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 08 Dec 2021 14:35:06: #3 Call peaks... INFO @ Wed, 08 Dec 2021 14:35:06: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Wed, 08 Dec 2021 14:35:21: #3 Call peaks for each chromosome... INFO @ Wed, 08 Dec 2021 14:35:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.20_peaks.xls INFO @ Wed, 08 Dec 2021 14:35:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.20_peaks.narrowPeak INFO @ Wed, 08 Dec 2021 14:35:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX10641217/SRX10641217.20_summits.bed INFO @ Wed, 08 Dec 2021 14:35:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (245 records, 4 fields): 1 millis CompletedMACS2peakCalling