Job ID = 6367837 SRX = SRX4085405 Genome = ce11 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-06-15T23:38:14 prefetch.2.10.7: 1) Downloading 'SRR7167434'... 2020-06-15T23:38:14 prefetch.2.10.7: Downloading via HTTPS... 2020-06-15T23:49:23 prefetch.2.10.7: HTTPS download succeed 2020-06-15T23:49:24 prefetch.2.10.7: 1) 'SRR7167434' was downloaded successfully Read 19278998 spots for SRR7167434/SRR7167434.sra Written 19278998 spots for SRR7167434/SRR7167434.sra 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: 00:15:25 19278998 reads; of these: 19278998 (100.00%) were paired; of these: 869003 (4.51%) aligned concordantly 0 times 16344127 (84.78%) aligned concordantly exactly 1 time 2065868 (10.72%) aligned concordantly >1 times ---- 869003 pairs aligned concordantly 0 times; of these: 238949 (27.50%) aligned discordantly 1 time ---- 630054 pairs aligned 0 times concordantly or discordantly; of these: 1260108 mates make up the pairs; of these: 710416 (56.38%) aligned 0 times 430802 (34.19%) aligned exactly 1 time 118890 (9.43%) aligned >1 times 98.16% overall alignment rate Time searching: 00:15:25 Overall time: 00:15:25 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] 5596183 / 18554834 = 0.3016 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/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:16:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.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 @ Tue, 16 Jun 2020 09:16:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:16:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:16:52: 1000000 INFO @ Tue, 16 Jun 2020 09:16:57: 2000000 INFO @ Tue, 16 Jun 2020 09:17:02: 3000000 INFO @ Tue, 16 Jun 2020 09:17:08: 4000000 INFO @ Tue, 16 Jun 2020 09:17:13: 5000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:17:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.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 @ Tue, 16 Jun 2020 09:17:16: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:17:16: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:17:19: 6000000 INFO @ Tue, 16 Jun 2020 09:17:23: 1000000 INFO @ Tue, 16 Jun 2020 09:17:25: 7000000 INFO @ Tue, 16 Jun 2020 09:17:29: 2000000 INFO @ Tue, 16 Jun 2020 09:17:30: 8000000 INFO @ Tue, 16 Jun 2020 09:17:35: 3000000 INFO @ Tue, 16 Jun 2020 09:17:36: 9000000 INFO @ Tue, 16 Jun 2020 09:17:41: 4000000 INFO @ Tue, 16 Jun 2020 09:17:43: 10000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Tue, 16 Jun 2020 09:17:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.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 @ Tue, 16 Jun 2020 09:17:47: #1 read tag files... INFO @ Tue, 16 Jun 2020 09:17:47: #1 read treatment tags... INFO @ Tue, 16 Jun 2020 09:17:48: 5000000 INFO @ Tue, 16 Jun 2020 09:17:49: 11000000 INFO @ Tue, 16 Jun 2020 09:17:53: 1000000 INFO @ Tue, 16 Jun 2020 09:17:55: 6000000 INFO @ Tue, 16 Jun 2020 09:17:55: 12000000 INFO @ Tue, 16 Jun 2020 09:17:59: 2000000 INFO @ Tue, 16 Jun 2020 09:18:01: 7000000 INFO @ Tue, 16 Jun 2020 09:18:01: 13000000 INFO @ Tue, 16 Jun 2020 09:18:06: 3000000 INFO @ Tue, 16 Jun 2020 09:18:07: 8000000 INFO @ Tue, 16 Jun 2020 09:18:07: 14000000 INFO @ Tue, 16 Jun 2020 09:18:13: 4000000 INFO @ Tue, 16 Jun 2020 09:18:13: 9000000 INFO @ Tue, 16 Jun 2020 09:18:13: 15000000 INFO @ Tue, 16 Jun 2020 09:18:18: 10000000 INFO @ Tue, 16 Jun 2020 09:18:19: 5000000 INFO @ Tue, 16 Jun 2020 09:18:19: 16000000 INFO @ Tue, 16 Jun 2020 09:18:24: 11000000 INFO @ Tue, 16 Jun 2020 09:18:25: 17000000 INFO @ Tue, 16 Jun 2020 09:18:25: 6000000 INFO @ Tue, 16 Jun 2020 09:18:31: 18000000 INFO @ Tue, 16 Jun 2020 09:18:31: 12000000 INFO @ Tue, 16 Jun 2020 09:18:32: 7000000 INFO @ Tue, 16 Jun 2020 09:18:36: 19000000 INFO @ Tue, 16 Jun 2020 09:18:37: 13000000 INFO @ Tue, 16 Jun 2020 09:18:38: 8000000 INFO @ Tue, 16 Jun 2020 09:18:43: 20000000 INFO @ Tue, 16 Jun 2020 09:18:43: 14000000 INFO @ Tue, 16 Jun 2020 09:18:45: 9000000 INFO @ Tue, 16 Jun 2020 09:18:49: 21000000 INFO @ Tue, 16 Jun 2020 09:18:50: 15000000 INFO @ Tue, 16 Jun 2020 09:18:52: 10000000 INFO @ Tue, 16 Jun 2020 09:18:55: 22000000 INFO @ Tue, 16 Jun 2020 09:18:56: 16000000 INFO @ Tue, 16 Jun 2020 09:18:59: 11000000 INFO @ Tue, 16 Jun 2020 09:19:01: 23000000 INFO @ Tue, 16 Jun 2020 09:19:02: 17000000 INFO @ Tue, 16 Jun 2020 09:19:05: 12000000 INFO @ Tue, 16 Jun 2020 09:19:07: 24000000 INFO @ Tue, 16 Jun 2020 09:19:09: 18000000 INFO @ Tue, 16 Jun 2020 09:19:10: 13000000 INFO @ Tue, 16 Jun 2020 09:19:13: 25000000 INFO @ Tue, 16 Jun 2020 09:19:15: 19000000 INFO @ Tue, 16 Jun 2020 09:19:16: 14000000 INFO @ Tue, 16 Jun 2020 09:19:19: 26000000 INFO @ Tue, 16 Jun 2020 09:19:21: 20000000 INFO @ Tue, 16 Jun 2020 09:19:22: 15000000 INFO @ Tue, 16 Jun 2020 09:19:23: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:19:23: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:19:23: #1 total tags in treatment: 12841687 INFO @ Tue, 16 Jun 2020 09:19:23: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:19:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:19:24: #1 tags after filtering in treatment: 11021083 INFO @ Tue, 16 Jun 2020 09:19:24: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:19:24: #1 finished! INFO @ Tue, 16 Jun 2020 09:19:24: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:19:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:19:24: #2 number of paired peaks: 190 WARNING @ Tue, 16 Jun 2020 09:19:24: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Tue, 16 Jun 2020 09:19:24: start model_add_line... INFO @ Tue, 16 Jun 2020 09:19:24: start X-correlation... INFO @ Tue, 16 Jun 2020 09:19:24: end of X-cor INFO @ Tue, 16 Jun 2020 09:19:24: #2 finished! INFO @ Tue, 16 Jun 2020 09:19:24: #2 predicted fragment length is 93 bps INFO @ Tue, 16 Jun 2020 09:19:24: #2 alternative fragment length(s) may be 3,93,113,597 bps INFO @ Tue, 16 Jun 2020 09:19:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.05_model.r WARNING @ Tue, 16 Jun 2020 09:19:24: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:19:24: #2 You may need to consider one of the other alternative d(s): 3,93,113,597 WARNING @ Tue, 16 Jun 2020 09:19:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:19:24: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:19:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:19:28: 21000000 INFO @ Tue, 16 Jun 2020 09:19:28: 16000000 INFO @ Tue, 16 Jun 2020 09:19:34: 17000000 INFO @ Tue, 16 Jun 2020 09:19:34: 22000000 INFO @ Tue, 16 Jun 2020 09:19:40: 18000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 16 Jun 2020 09:19:41: 23000000 INFO @ Tue, 16 Jun 2020 09:19:46: 19000000 INFO @ Tue, 16 Jun 2020 09:19:47: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:19:47: 24000000 INFO @ Tue, 16 Jun 2020 09:19:52: 20000000 INFO @ Tue, 16 Jun 2020 09:19:54: 25000000 INFO @ Tue, 16 Jun 2020 09:19:58: 21000000 INFO @ Tue, 16 Jun 2020 09:20:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.05_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.05_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.05_summits.bed INFO @ Tue, 16 Jun 2020 09:20:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3897 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:20:01: 26000000 INFO @ Tue, 16 Jun 2020 09:20:04: 22000000 INFO @ Tue, 16 Jun 2020 09:20:05: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:20:05: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:20:05: #1 total tags in treatment: 12841687 INFO @ Tue, 16 Jun 2020 09:20:05: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:20:05: #1 tags after filtering in treatment: 11021083 INFO @ Tue, 16 Jun 2020 09:20:05: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:20:05: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:05: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:06: #2 number of paired peaks: 190 WARNING @ Tue, 16 Jun 2020 09:20:06: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:06: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:06: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:06: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:06: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:06: #2 predicted fragment length is 93 bps INFO @ Tue, 16 Jun 2020 09:20:06: #2 alternative fragment length(s) may be 3,93,113,597 bps INFO @ Tue, 16 Jun 2020 09:20:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.10_model.r WARNING @ Tue, 16 Jun 2020 09:20:06: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:06: #2 You may need to consider one of the other alternative d(s): 3,93,113,597 WARNING @ Tue, 16 Jun 2020 09:20:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:20:06: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:10: 23000000 INFO @ Tue, 16 Jun 2020 09:20:15: 24000000 INFO @ Tue, 16 Jun 2020 09:20:21: 25000000 INFO @ Tue, 16 Jun 2020 09:20:27: 26000000 BigWig に変換しました。 INFO @ Tue, 16 Jun 2020 09:20:29: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:20:30: #1 tag size is determined as 51 bps INFO @ Tue, 16 Jun 2020 09:20:30: #1 tag size = 51 INFO @ Tue, 16 Jun 2020 09:20:30: #1 total tags in treatment: 12841687 INFO @ Tue, 16 Jun 2020 09:20:30: #1 user defined the maximum tags... INFO @ Tue, 16 Jun 2020 09:20:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 16 Jun 2020 09:20:31: #1 tags after filtering in treatment: 11021083 INFO @ Tue, 16 Jun 2020 09:20:31: #1 Redundant rate of treatment: 0.14 INFO @ Tue, 16 Jun 2020 09:20:31: #1 finished! INFO @ Tue, 16 Jun 2020 09:20:31: #2 Build Peak Model... INFO @ Tue, 16 Jun 2020 09:20:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 16 Jun 2020 09:20:31: #2 number of paired peaks: 190 WARNING @ Tue, 16 Jun 2020 09:20:31: Fewer paired peaks (190) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 190 pairs to build model! INFO @ Tue, 16 Jun 2020 09:20:31: start model_add_line... INFO @ Tue, 16 Jun 2020 09:20:31: start X-correlation... INFO @ Tue, 16 Jun 2020 09:20:31: end of X-cor INFO @ Tue, 16 Jun 2020 09:20:31: #2 finished! INFO @ Tue, 16 Jun 2020 09:20:31: #2 predicted fragment length is 93 bps INFO @ Tue, 16 Jun 2020 09:20:31: #2 alternative fragment length(s) may be 3,93,113,597 bps INFO @ Tue, 16 Jun 2020 09:20:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.20_model.r WARNING @ Tue, 16 Jun 2020 09:20:31: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 16 Jun 2020 09:20:31: #2 You may need to consider one of the other alternative d(s): 3,93,113,597 WARNING @ Tue, 16 Jun 2020 09:20:31: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 16 Jun 2020 09:20:31: #3 Call peaks... INFO @ Tue, 16 Jun 2020 09:20:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 16 Jun 2020 09:20:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.10_peaks.xls INFO @ Tue, 16 Jun 2020 09:20:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.10_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:20:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.10_summits.bed INFO @ Tue, 16 Jun 2020 09:20:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1432 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 16 Jun 2020 09:20:54: #3 Call peaks for each chromosome... INFO @ Tue, 16 Jun 2020 09:21:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.20_peaks.xls INFO @ Tue, 16 Jun 2020 09:21:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.20_peaks.narrowPeak INFO @ Tue, 16 Jun 2020 09:21:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce11/SRX4085405/SRX4085405.20_summits.bed INFO @ Tue, 16 Jun 2020 09:21:06: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (242 records, 4 fields): 1 millis CompletedMACS2peakCalling