Job ID = 12264821 SRX = SRX7687144 Genome = ce10 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... Read 27010582 spots for SRR11034887/SRR11034887.sra Written 27010582 spots for SRR11034887/SRR11034887.sra fastq に変換しました。 bowtie でマッピング中... Your job 12265571 ("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: 01:13:16 27010582 reads; of these: 27010582 (100.00%) were paired; of these: 5088151 (18.84%) aligned concordantly 0 times 14462020 (53.54%) aligned concordantly exactly 1 time 7460411 (27.62%) aligned concordantly >1 times ---- 5088151 pairs aligned concordantly 0 times; of these: 3689128 (72.50%) aligned discordantly 1 time ---- 1399023 pairs aligned 0 times concordantly or discordantly; of these: 2798046 mates make up the pairs; of these: 1188982 (42.49%) aligned 0 times 592905 (21.19%) aligned exactly 1 time 1016159 (36.32%) aligned >1 times 97.80% overall alignment rate Time searching: 01:13:17 Overall time: 01:13:17 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 24 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] 7779431 / 25565767 = 0.3043 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 07:30:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.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 07:30:09: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:30:09: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:30:15: 1000000 INFO @ Sat, 03 Apr 2021 07:30:20: 2000000 INFO @ Sat, 03 Apr 2021 07:30:27: 3000000 INFO @ Sat, 03 Apr 2021 07:30:33: 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 07:30:39: 5000000 INFO @ Sat, 03 Apr 2021 07:30:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.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 07:30:39: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:30:39: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:30:45: 6000000 INFO @ Sat, 03 Apr 2021 07:30:46: 1000000 INFO @ Sat, 03 Apr 2021 07:30:51: 7000000 INFO @ Sat, 03 Apr 2021 07:30:52: 2000000 INFO @ Sat, 03 Apr 2021 07:30:56: 8000000 INFO @ Sat, 03 Apr 2021 07:30:59: 3000000 INFO @ Sat, 03 Apr 2021 07:31:02: 9000000 INFO @ Sat, 03 Apr 2021 07:31:05: 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 07:31:08: 10000000 INFO @ Sat, 03 Apr 2021 07:31:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.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 07:31:09: #1 read tag files... INFO @ Sat, 03 Apr 2021 07:31:09: #1 read treatment tags... INFO @ Sat, 03 Apr 2021 07:31:11: 5000000 INFO @ Sat, 03 Apr 2021 07:31:15: 11000000 INFO @ Sat, 03 Apr 2021 07:31:15: 1000000 INFO @ Sat, 03 Apr 2021 07:31:18: 6000000 INFO @ Sat, 03 Apr 2021 07:31:21: 12000000 INFO @ Sat, 03 Apr 2021 07:31:21: 2000000 INFO @ Sat, 03 Apr 2021 07:31:24: 7000000 INFO @ Sat, 03 Apr 2021 07:31:27: 3000000 INFO @ Sat, 03 Apr 2021 07:31:28: 13000000 INFO @ Sat, 03 Apr 2021 07:31:30: 8000000 INFO @ Sat, 03 Apr 2021 07:31:33: 4000000 INFO @ Sat, 03 Apr 2021 07:31:34: 14000000 INFO @ Sat, 03 Apr 2021 07:31:36: 9000000 INFO @ Sat, 03 Apr 2021 07:31:39: 5000000 INFO @ Sat, 03 Apr 2021 07:31:40: 15000000 INFO @ Sat, 03 Apr 2021 07:31:43: 10000000 INFO @ Sat, 03 Apr 2021 07:31:45: 6000000 INFO @ Sat, 03 Apr 2021 07:31:47: 16000000 INFO @ Sat, 03 Apr 2021 07:31:50: 11000000 INFO @ Sat, 03 Apr 2021 07:31:51: 7000000 INFO @ Sat, 03 Apr 2021 07:31:53: 17000000 INFO @ Sat, 03 Apr 2021 07:31:56: 12000000 INFO @ Sat, 03 Apr 2021 07:31:56: 8000000 INFO @ Sat, 03 Apr 2021 07:32:00: 18000000 INFO @ Sat, 03 Apr 2021 07:32:03: 9000000 INFO @ Sat, 03 Apr 2021 07:32:04: 13000000 INFO @ Sat, 03 Apr 2021 07:32:07: 19000000 INFO @ Sat, 03 Apr 2021 07:32:09: 10000000 INFO @ Sat, 03 Apr 2021 07:32:10: 14000000 INFO @ Sat, 03 Apr 2021 07:32:13: 20000000 INFO @ Sat, 03 Apr 2021 07:32:14: 11000000 INFO @ Sat, 03 Apr 2021 07:32:17: 15000000 INFO @ Sat, 03 Apr 2021 07:32:19: 21000000 INFO @ Sat, 03 Apr 2021 07:32:20: 12000000 INFO @ Sat, 03 Apr 2021 07:32:24: 16000000 INFO @ Sat, 03 Apr 2021 07:32:26: 13000000 INFO @ Sat, 03 Apr 2021 07:32:27: 22000000 INFO @ Sat, 03 Apr 2021 07:32:30: 17000000 INFO @ Sat, 03 Apr 2021 07:32:32: 14000000 INFO @ Sat, 03 Apr 2021 07:32:33: 23000000 INFO @ Sat, 03 Apr 2021 07:32:36: 18000000 INFO @ Sat, 03 Apr 2021 07:32:38: 15000000 INFO @ Sat, 03 Apr 2021 07:32:39: 24000000 INFO @ Sat, 03 Apr 2021 07:32:43: 19000000 INFO @ Sat, 03 Apr 2021 07:32:44: 16000000 INFO @ Sat, 03 Apr 2021 07:32:46: 25000000 INFO @ Sat, 03 Apr 2021 07:32:50: 20000000 INFO @ Sat, 03 Apr 2021 07:32:51: 17000000 INFO @ Sat, 03 Apr 2021 07:32:53: 26000000 INFO @ Sat, 03 Apr 2021 07:32:56: 21000000 INFO @ Sat, 03 Apr 2021 07:32:57: 18000000 INFO @ Sat, 03 Apr 2021 07:32:59: 27000000 INFO @ Sat, 03 Apr 2021 07:33:03: 22000000 INFO @ Sat, 03 Apr 2021 07:33:04: 19000000 INFO @ Sat, 03 Apr 2021 07:33:07: 28000000 INFO @ Sat, 03 Apr 2021 07:33:10: 23000000 INFO @ Sat, 03 Apr 2021 07:33:11: 20000000 INFO @ Sat, 03 Apr 2021 07:33:14: 29000000 INFO @ Sat, 03 Apr 2021 07:33:16: 24000000 INFO @ Sat, 03 Apr 2021 07:33:17: 21000000 INFO @ Sat, 03 Apr 2021 07:33:21: 30000000 INFO @ Sat, 03 Apr 2021 07:33:23: 22000000 INFO @ Sat, 03 Apr 2021 07:33:23: 25000000 INFO @ Sat, 03 Apr 2021 07:33:29: 31000000 INFO @ Sat, 03 Apr 2021 07:33:29: 23000000 INFO @ Sat, 03 Apr 2021 07:33:30: 26000000 INFO @ Sat, 03 Apr 2021 07:33:35: 24000000 INFO @ Sat, 03 Apr 2021 07:33:36: 32000000 INFO @ Sat, 03 Apr 2021 07:33:38: 27000000 INFO @ Sat, 03 Apr 2021 07:33:41: 25000000 INFO @ Sat, 03 Apr 2021 07:33:44: 33000000 INFO @ Sat, 03 Apr 2021 07:33:45: 28000000 INFO @ Sat, 03 Apr 2021 07:33:47: 26000000 INFO @ Sat, 03 Apr 2021 07:33:52: 34000000 INFO @ Sat, 03 Apr 2021 07:33:53: 29000000 INFO @ Sat, 03 Apr 2021 07:33:53: 27000000 INFO @ Sat, 03 Apr 2021 07:33:59: 28000000 INFO @ Sat, 03 Apr 2021 07:34:00: 35000000 INFO @ Sat, 03 Apr 2021 07:34:01: 30000000 INFO @ Sat, 03 Apr 2021 07:34:06: 29000000 INFO @ Sat, 03 Apr 2021 07:34:08: 36000000 INFO @ Sat, 03 Apr 2021 07:34:10: 31000000 INFO @ Sat, 03 Apr 2021 07:34:13: 30000000 INFO @ Sat, 03 Apr 2021 07:34:16: 37000000 INFO @ Sat, 03 Apr 2021 07:34:18: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:34:18: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:34:18: #1 total tags in treatment: 14788112 INFO @ Sat, 03 Apr 2021 07:34:18: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:34:18: #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 07:34:18: 32000000 INFO @ Sat, 03 Apr 2021 07:34:18: #1 tags after filtering in treatment: 10327317 INFO @ Sat, 03 Apr 2021 07:34:18: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 07:34:18: #1 finished! INFO @ Sat, 03 Apr 2021 07:34:18: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:34:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:34:19: #2 number of paired peaks: 479 WARNING @ Sat, 03 Apr 2021 07:34:19: Fewer paired peaks (479) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 479 pairs to build model! INFO @ Sat, 03 Apr 2021 07:34:19: start model_add_line... INFO @ Sat, 03 Apr 2021 07:34:19: start X-correlation... INFO @ Sat, 03 Apr 2021 07:34:19: end of X-cor INFO @ Sat, 03 Apr 2021 07:34:19: #2 finished! INFO @ Sat, 03 Apr 2021 07:34:19: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Apr 2021 07:34:19: #2 alternative fragment length(s) may be 4,109,123 bps INFO @ Sat, 03 Apr 2021 07:34:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.05_model.r WARNING @ Sat, 03 Apr 2021 07:34:19: #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 07:34:19: #2 You may need to consider one of the other alternative d(s): 4,109,123 WARNING @ Sat, 03 Apr 2021 07:34:19: #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 07:34:19: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:34:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:34:20: 31000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Apr 2021 07:34:25: 32000000 INFO @ Sat, 03 Apr 2021 07:34:26: 33000000 INFO @ Sat, 03 Apr 2021 07:34:31: 33000000 INFO @ Sat, 03 Apr 2021 07:34:34: 34000000 INFO @ Sat, 03 Apr 2021 07:34:36: 34000000 INFO @ Sat, 03 Apr 2021 07:34:40: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:34:42: 35000000 INFO @ Sat, 03 Apr 2021 07:34:42: 35000000 INFO @ Sat, 03 Apr 2021 07:34:47: 36000000 INFO @ Sat, 03 Apr 2021 07:34:50: 36000000 INFO @ Sat, 03 Apr 2021 07:34:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.05_peaks.xls INFO @ Sat, 03 Apr 2021 07:34:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.05_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:34:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.05_summits.bed INFO @ Sat, 03 Apr 2021 07:34:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (682 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Apr 2021 07:34:52: 37000000 INFO @ Sat, 03 Apr 2021 07:34:54: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:34:54: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:34:54: #1 total tags in treatment: 14788112 INFO @ Sat, 03 Apr 2021 07:34:54: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:34:54: #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 07:34:54: #1 tags after filtering in treatment: 10327317 INFO @ Sat, 03 Apr 2021 07:34:54: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 07:34:54: #1 finished! INFO @ Sat, 03 Apr 2021 07:34:54: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:34:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:34:55: #2 number of paired peaks: 479 WARNING @ Sat, 03 Apr 2021 07:34:55: Fewer paired peaks (479) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 479 pairs to build model! INFO @ Sat, 03 Apr 2021 07:34:55: start model_add_line... INFO @ Sat, 03 Apr 2021 07:34:55: start X-correlation... INFO @ Sat, 03 Apr 2021 07:34:55: end of X-cor INFO @ Sat, 03 Apr 2021 07:34:55: #2 finished! INFO @ Sat, 03 Apr 2021 07:34:55: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Apr 2021 07:34:55: #2 alternative fragment length(s) may be 4,109,123 bps INFO @ Sat, 03 Apr 2021 07:34:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.20_model.r WARNING @ Sat, 03 Apr 2021 07:34:55: #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 07:34:55: #2 You may need to consider one of the other alternative d(s): 4,109,123 WARNING @ Sat, 03 Apr 2021 07:34:55: #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 07:34:55: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:34:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:34:57: 37000000 INFO @ Sat, 03 Apr 2021 07:34:59: #1 tag size is determined as 75 bps INFO @ Sat, 03 Apr 2021 07:34:59: #1 tag size = 75 INFO @ Sat, 03 Apr 2021 07:34:59: #1 total tags in treatment: 14788112 INFO @ Sat, 03 Apr 2021 07:34:59: #1 user defined the maximum tags... INFO @ Sat, 03 Apr 2021 07:34:59: #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 07:35:00: #1 tags after filtering in treatment: 10327317 INFO @ Sat, 03 Apr 2021 07:35:00: #1 Redundant rate of treatment: 0.30 INFO @ Sat, 03 Apr 2021 07:35:00: #1 finished! INFO @ Sat, 03 Apr 2021 07:35:00: #2 Build Peak Model... INFO @ Sat, 03 Apr 2021 07:35:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 03 Apr 2021 07:35:01: #2 number of paired peaks: 479 WARNING @ Sat, 03 Apr 2021 07:35:01: Fewer paired peaks (479) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 479 pairs to build model! INFO @ Sat, 03 Apr 2021 07:35:01: start model_add_line... INFO @ Sat, 03 Apr 2021 07:35:01: start X-correlation... INFO @ Sat, 03 Apr 2021 07:35:01: end of X-cor INFO @ Sat, 03 Apr 2021 07:35:01: #2 finished! INFO @ Sat, 03 Apr 2021 07:35:01: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Apr 2021 07:35:01: #2 alternative fragment length(s) may be 4,109,123 bps INFO @ Sat, 03 Apr 2021 07:35:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.10_model.r WARNING @ Sat, 03 Apr 2021 07:35:01: #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 07:35:01: #2 You may need to consider one of the other alternative d(s): 4,109,123 WARNING @ Sat, 03 Apr 2021 07:35:01: #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 07:35:01: #3 Call peaks... INFO @ Sat, 03 Apr 2021 07:35:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Apr 2021 07:35:15: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:35:21: #3 Call peaks for each chromosome... INFO @ Sat, 03 Apr 2021 07:35:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.20_peaks.xls INFO @ Sat, 03 Apr 2021 07:35:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.20_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:35:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.20_summits.bed INFO @ Sat, 03 Apr 2021 07:35:24: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (206 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Apr 2021 07:35:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.10_peaks.xls INFO @ Sat, 03 Apr 2021 07:35:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.10_peaks.narrowPeak INFO @ Sat, 03 Apr 2021 07:35:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX7687144/SRX7687144.10_summits.bed INFO @ Sat, 03 Apr 2021 07:35:31: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (377 records, 4 fields): 5 millis CompletedMACS2peakCalling