Job ID = 5720167 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-15T12:53:47 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T12:54:32 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T13:05:33 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T13:12:00 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T13:25:04 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) 2020-04-15T13:27:19 fasterq-dump.2.9.6 sys: timeout exhausted while reading file within network system module - mbedtls_ssl_read returned -76 ( NET - Reading information from the socket failed ) spots read : 39,995,409 reads read : 79,990,818 reads written : 79,990,818 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 01:17:49 39995409 reads; of these: 39995409 (100.00%) were paired; of these: 20330876 (50.83%) aligned concordantly 0 times 16135655 (40.34%) aligned concordantly exactly 1 time 3528878 (8.82%) aligned concordantly >1 times ---- 20330876 pairs aligned concordantly 0 times; of these: 10206523 (50.20%) aligned discordantly 1 time ---- 10124353 pairs aligned 0 times concordantly or discordantly; of these: 20248706 mates make up the pairs; of these: 16300667 (80.50%) aligned 0 times 1675412 (8.27%) aligned exactly 1 time 2272627 (11.22%) aligned >1 times 79.62% overall alignment rate Time searching: 01:17:49 Overall time: 01:17:49 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 48 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] 4044192 / 29218853 = 0.1384 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 @ Thu, 16 Apr 2020 00:21:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.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 @ Thu, 16 Apr 2020 00:21:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:21:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:21:14: 1000000 INFO @ Thu, 16 Apr 2020 00:21:23: 2000000 INFO @ Thu, 16 Apr 2020 00:21:31: 3000000 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 @ Thu, 16 Apr 2020 00:21:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.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 @ Thu, 16 Apr 2020 00:21:35: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:21:35: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:21:40: 4000000 INFO @ Thu, 16 Apr 2020 00:21:45: 1000000 INFO @ Thu, 16 Apr 2020 00:21:50: 5000000 INFO @ Thu, 16 Apr 2020 00:21:54: 2000000 INFO @ Thu, 16 Apr 2020 00:21:59: 6000000 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 @ Thu, 16 Apr 2020 00:22:04: 3000000 INFO @ Thu, 16 Apr 2020 00:22:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.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 @ Thu, 16 Apr 2020 00:22:05: #1 read tag files... INFO @ Thu, 16 Apr 2020 00:22:05: #1 read treatment tags... INFO @ Thu, 16 Apr 2020 00:22:09: 7000000 INFO @ Thu, 16 Apr 2020 00:22:14: 4000000 INFO @ Thu, 16 Apr 2020 00:22:15: 1000000 INFO @ Thu, 16 Apr 2020 00:22:18: 8000000 INFO @ Thu, 16 Apr 2020 00:22:23: 5000000 INFO @ Thu, 16 Apr 2020 00:22:25: 2000000 INFO @ Thu, 16 Apr 2020 00:22:28: 9000000 INFO @ Thu, 16 Apr 2020 00:22:33: 6000000 INFO @ Thu, 16 Apr 2020 00:22:35: 3000000 INFO @ Thu, 16 Apr 2020 00:22:37: 10000000 INFO @ Thu, 16 Apr 2020 00:22:43: 7000000 INFO @ Thu, 16 Apr 2020 00:22:44: 4000000 INFO @ Thu, 16 Apr 2020 00:22:46: 11000000 INFO @ Thu, 16 Apr 2020 00:22:52: 8000000 INFO @ Thu, 16 Apr 2020 00:22:53: 5000000 INFO @ Thu, 16 Apr 2020 00:22:56: 12000000 INFO @ Thu, 16 Apr 2020 00:23:02: 9000000 INFO @ Thu, 16 Apr 2020 00:23:03: 6000000 INFO @ Thu, 16 Apr 2020 00:23:05: 13000000 INFO @ Thu, 16 Apr 2020 00:23:11: 10000000 INFO @ Thu, 16 Apr 2020 00:23:12: 7000000 INFO @ Thu, 16 Apr 2020 00:23:15: 14000000 INFO @ Thu, 16 Apr 2020 00:23:21: 11000000 INFO @ Thu, 16 Apr 2020 00:23:22: 8000000 INFO @ Thu, 16 Apr 2020 00:23:24: 15000000 INFO @ Thu, 16 Apr 2020 00:23:30: 12000000 INFO @ Thu, 16 Apr 2020 00:23:31: 9000000 INFO @ Thu, 16 Apr 2020 00:23:33: 16000000 INFO @ Thu, 16 Apr 2020 00:23:40: 10000000 INFO @ Thu, 16 Apr 2020 00:23:41: 13000000 INFO @ Thu, 16 Apr 2020 00:23:43: 17000000 INFO @ Thu, 16 Apr 2020 00:23:50: 11000000 INFO @ Thu, 16 Apr 2020 00:23:50: 14000000 INFO @ Thu, 16 Apr 2020 00:23:52: 18000000 INFO @ Thu, 16 Apr 2020 00:23:59: 12000000 INFO @ Thu, 16 Apr 2020 00:23:59: 15000000 INFO @ Thu, 16 Apr 2020 00:24:01: 19000000 INFO @ Thu, 16 Apr 2020 00:24:09: 16000000 INFO @ Thu, 16 Apr 2020 00:24:09: 13000000 INFO @ Thu, 16 Apr 2020 00:24:11: 20000000 INFO @ Thu, 16 Apr 2020 00:24:19: 17000000 INFO @ Thu, 16 Apr 2020 00:24:20: 21000000 INFO @ Thu, 16 Apr 2020 00:24:20: 14000000 INFO @ Thu, 16 Apr 2020 00:24:29: 18000000 INFO @ Thu, 16 Apr 2020 00:24:29: 22000000 INFO @ Thu, 16 Apr 2020 00:24:30: 15000000 INFO @ Thu, 16 Apr 2020 00:24:38: 23000000 INFO @ Thu, 16 Apr 2020 00:24:39: 19000000 INFO @ Thu, 16 Apr 2020 00:24:41: 16000000 INFO @ Thu, 16 Apr 2020 00:24:47: 24000000 INFO @ Thu, 16 Apr 2020 00:24:49: 20000000 INFO @ Thu, 16 Apr 2020 00:24:51: 17000000 INFO @ Thu, 16 Apr 2020 00:24:56: 25000000 INFO @ Thu, 16 Apr 2020 00:24:59: 21000000 INFO @ Thu, 16 Apr 2020 00:25:01: 18000000 INFO @ Thu, 16 Apr 2020 00:25:05: 26000000 INFO @ Thu, 16 Apr 2020 00:25:08: 22000000 INFO @ Thu, 16 Apr 2020 00:25:10: 19000000 INFO @ Thu, 16 Apr 2020 00:25:14: 27000000 INFO @ Thu, 16 Apr 2020 00:25:18: 23000000 INFO @ Thu, 16 Apr 2020 00:25:20: 20000000 INFO @ Thu, 16 Apr 2020 00:25:24: 28000000 INFO @ Thu, 16 Apr 2020 00:25:28: 24000000 INFO @ Thu, 16 Apr 2020 00:25:30: 21000000 INFO @ Thu, 16 Apr 2020 00:25:32: 29000000 INFO @ Thu, 16 Apr 2020 00:25:37: 25000000 INFO @ Thu, 16 Apr 2020 00:25:40: 22000000 INFO @ Thu, 16 Apr 2020 00:25:41: 30000000 INFO @ Thu, 16 Apr 2020 00:25:47: 26000000 INFO @ Thu, 16 Apr 2020 00:25:50: 23000000 INFO @ Thu, 16 Apr 2020 00:25:50: 31000000 INFO @ Thu, 16 Apr 2020 00:25:57: 27000000 INFO @ Thu, 16 Apr 2020 00:25:59: 32000000 INFO @ Thu, 16 Apr 2020 00:26:01: 24000000 INFO @ Thu, 16 Apr 2020 00:26:07: 28000000 INFO @ Thu, 16 Apr 2020 00:26:08: 33000000 INFO @ Thu, 16 Apr 2020 00:26:11: 25000000 INFO @ Thu, 16 Apr 2020 00:26:17: 29000000 INFO @ Thu, 16 Apr 2020 00:26:17: 34000000 INFO @ Thu, 16 Apr 2020 00:26:21: 26000000 INFO @ Thu, 16 Apr 2020 00:26:25: 35000000 INFO @ Thu, 16 Apr 2020 00:26:27: 30000000 INFO @ Thu, 16 Apr 2020 00:26:30: 27000000 INFO @ Thu, 16 Apr 2020 00:26:34: 36000000 INFO @ Thu, 16 Apr 2020 00:26:36: 31000000 INFO @ Thu, 16 Apr 2020 00:26:40: 28000000 INFO @ Thu, 16 Apr 2020 00:26:43: 37000000 INFO @ Thu, 16 Apr 2020 00:26:46: 32000000 INFO @ Thu, 16 Apr 2020 00:26:50: 29000000 INFO @ Thu, 16 Apr 2020 00:26:52: 38000000 INFO @ Thu, 16 Apr 2020 00:26:56: 33000000 INFO @ Thu, 16 Apr 2020 00:27:00: 30000000 INFO @ Thu, 16 Apr 2020 00:27:01: 39000000 INFO @ Thu, 16 Apr 2020 00:27:05: 34000000 INFO @ Thu, 16 Apr 2020 00:27:10: 40000000 INFO @ Thu, 16 Apr 2020 00:27:10: 31000000 INFO @ Thu, 16 Apr 2020 00:27:15: 35000000 INFO @ Thu, 16 Apr 2020 00:27:19: 41000000 INFO @ Thu, 16 Apr 2020 00:27:19: 32000000 INFO @ Thu, 16 Apr 2020 00:27:24: 36000000 INFO @ Thu, 16 Apr 2020 00:27:28: 42000000 INFO @ Thu, 16 Apr 2020 00:27:28: 33000000 INFO @ Thu, 16 Apr 2020 00:27:33: 37000000 INFO @ Thu, 16 Apr 2020 00:27:37: 43000000 INFO @ Thu, 16 Apr 2020 00:27:38: 34000000 INFO @ Thu, 16 Apr 2020 00:27:43: 38000000 INFO @ Thu, 16 Apr 2020 00:27:45: 44000000 INFO @ Thu, 16 Apr 2020 00:27:48: 35000000 INFO @ Thu, 16 Apr 2020 00:27:52: 39000000 INFO @ Thu, 16 Apr 2020 00:27:54: 45000000 INFO @ Thu, 16 Apr 2020 00:27:57: 36000000 INFO @ Thu, 16 Apr 2020 00:28:01: 40000000 INFO @ Thu, 16 Apr 2020 00:28:04: 46000000 INFO @ Thu, 16 Apr 2020 00:28:06: 37000000 INFO @ Thu, 16 Apr 2020 00:28:11: 41000000 INFO @ Thu, 16 Apr 2020 00:28:13: 47000000 INFO @ Thu, 16 Apr 2020 00:28:15: 38000000 INFO @ Thu, 16 Apr 2020 00:28:20: 42000000 INFO @ Thu, 16 Apr 2020 00:28:21: 48000000 INFO @ Thu, 16 Apr 2020 00:28:24: 39000000 INFO @ Thu, 16 Apr 2020 00:28:29: 43000000 INFO @ Thu, 16 Apr 2020 00:28:30: 49000000 INFO @ Thu, 16 Apr 2020 00:28:33: 40000000 INFO @ Thu, 16 Apr 2020 00:28:38: 44000000 INFO @ Thu, 16 Apr 2020 00:28:39: 50000000 INFO @ Thu, 16 Apr 2020 00:28:42: 41000000 INFO @ Thu, 16 Apr 2020 00:28:47: 45000000 INFO @ Thu, 16 Apr 2020 00:28:48: 51000000 INFO @ Thu, 16 Apr 2020 00:28:51: 42000000 INFO @ Thu, 16 Apr 2020 00:28:57: 46000000 INFO @ Thu, 16 Apr 2020 00:28:57: 52000000 INFO @ Thu, 16 Apr 2020 00:29:00: 43000000 INFO @ Thu, 16 Apr 2020 00:29:06: 47000000 INFO @ Thu, 16 Apr 2020 00:29:06: 53000000 INFO @ Thu, 16 Apr 2020 00:29:09: 44000000 INFO @ Thu, 16 Apr 2020 00:29:14: 54000000 INFO @ Thu, 16 Apr 2020 00:29:15: 48000000 INFO @ Thu, 16 Apr 2020 00:29:18: 45000000 INFO @ Thu, 16 Apr 2020 00:29:23: 55000000 INFO @ Thu, 16 Apr 2020 00:29:24: 49000000 INFO @ Thu, 16 Apr 2020 00:29:27: 46000000 INFO @ Thu, 16 Apr 2020 00:29:29: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 00:29:29: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 00:29:29: #1 total tags in treatment: 16738099 INFO @ Thu, 16 Apr 2020 00:29:29: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:29:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:29:29: #1 tags after filtering in treatment: 13757946 INFO @ Thu, 16 Apr 2020 00:29:29: #1 Redundant rate of treatment: 0.18 INFO @ Thu, 16 Apr 2020 00:29:29: #1 finished! INFO @ Thu, 16 Apr 2020 00:29:29: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:29:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:29:30: #2 number of paired peaks: 248 WARNING @ Thu, 16 Apr 2020 00:29:30: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Thu, 16 Apr 2020 00:29:30: start model_add_line... INFO @ Thu, 16 Apr 2020 00:29:30: start X-correlation... INFO @ Thu, 16 Apr 2020 00:29:30: end of X-cor INFO @ Thu, 16 Apr 2020 00:29:30: #2 finished! INFO @ Thu, 16 Apr 2020 00:29:30: #2 predicted fragment length is 196 bps INFO @ Thu, 16 Apr 2020 00:29:30: #2 alternative fragment length(s) may be 196,211 bps INFO @ Thu, 16 Apr 2020 00:29:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.05_model.r WARNING @ Thu, 16 Apr 2020 00:29:30: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:29:30: #2 You may need to consider one of the other alternative d(s): 196,211 WARNING @ Thu, 16 Apr 2020 00:29:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:29:30: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:29:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:29:33: 50000000 INFO @ Thu, 16 Apr 2020 00:29:36: 47000000 INFO @ Thu, 16 Apr 2020 00:29:42: 51000000 INFO @ Thu, 16 Apr 2020 00:29:45: 48000000 INFO @ Thu, 16 Apr 2020 00:29:51: 52000000 INFO @ Thu, 16 Apr 2020 00:29:53: 49000000 INFO @ Thu, 16 Apr 2020 00:30:00: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:30:01: 53000000 INFO @ Thu, 16 Apr 2020 00:30:02: 50000000 INFO @ Thu, 16 Apr 2020 00:30:10: 54000000 INFO @ Thu, 16 Apr 2020 00:30:11: 51000000 INFO @ Thu, 16 Apr 2020 00:30:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.05_peaks.xls INFO @ Thu, 16 Apr 2020 00:30:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.05_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:30:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.05_summits.bed INFO @ Thu, 16 Apr 2020 00:30:14: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (644 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:30:19: 55000000 INFO @ Thu, 16 Apr 2020 00:30:19: 52000000 INFO @ Thu, 16 Apr 2020 00:30:25: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 00:30:25: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 00:30:25: #1 total tags in treatment: 16738099 INFO @ Thu, 16 Apr 2020 00:30:25: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:30:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:30:26: #1 tags after filtering in treatment: 13757946 INFO @ Thu, 16 Apr 2020 00:30:26: #1 Redundant rate of treatment: 0.18 INFO @ Thu, 16 Apr 2020 00:30:26: #1 finished! INFO @ Thu, 16 Apr 2020 00:30:26: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:30:26: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:30:27: #2 number of paired peaks: 248 WARNING @ Thu, 16 Apr 2020 00:30:27: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Thu, 16 Apr 2020 00:30:27: start model_add_line... INFO @ Thu, 16 Apr 2020 00:30:27: start X-correlation... INFO @ Thu, 16 Apr 2020 00:30:27: end of X-cor INFO @ Thu, 16 Apr 2020 00:30:27: #2 finished! INFO @ Thu, 16 Apr 2020 00:30:27: #2 predicted fragment length is 196 bps INFO @ Thu, 16 Apr 2020 00:30:27: #2 alternative fragment length(s) may be 196,211 bps INFO @ Thu, 16 Apr 2020 00:30:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.10_model.r WARNING @ Thu, 16 Apr 2020 00:30:27: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:30:27: #2 You may need to consider one of the other alternative d(s): 196,211 WARNING @ Thu, 16 Apr 2020 00:30:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:30:27: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:30:27: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:30:27: 53000000 INFO @ Thu, 16 Apr 2020 00:30:35: 54000000 INFO @ Thu, 16 Apr 2020 00:30:44: 55000000 INFO @ Thu, 16 Apr 2020 00:30:49: #1 tag size is determined as 150 bps INFO @ Thu, 16 Apr 2020 00:30:49: #1 tag size = 150 INFO @ Thu, 16 Apr 2020 00:30:49: #1 total tags in treatment: 16738099 INFO @ Thu, 16 Apr 2020 00:30:49: #1 user defined the maximum tags... INFO @ Thu, 16 Apr 2020 00:30:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 16 Apr 2020 00:30:49: #1 tags after filtering in treatment: 13757946 INFO @ Thu, 16 Apr 2020 00:30:49: #1 Redundant rate of treatment: 0.18 INFO @ Thu, 16 Apr 2020 00:30:49: #1 finished! INFO @ Thu, 16 Apr 2020 00:30:49: #2 Build Peak Model... INFO @ Thu, 16 Apr 2020 00:30:49: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 16 Apr 2020 00:30:50: #2 number of paired peaks: 248 WARNING @ Thu, 16 Apr 2020 00:30:50: Fewer paired peaks (248) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 248 pairs to build model! INFO @ Thu, 16 Apr 2020 00:30:50: start model_add_line... INFO @ Thu, 16 Apr 2020 00:30:50: start X-correlation... INFO @ Thu, 16 Apr 2020 00:30:50: end of X-cor INFO @ Thu, 16 Apr 2020 00:30:50: #2 finished! INFO @ Thu, 16 Apr 2020 00:30:50: #2 predicted fragment length is 196 bps INFO @ Thu, 16 Apr 2020 00:30:50: #2 alternative fragment length(s) may be 196,211 bps INFO @ Thu, 16 Apr 2020 00:30:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.20_model.r WARNING @ Thu, 16 Apr 2020 00:30:50: #2 Since the d (196) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 16 Apr 2020 00:30:50: #2 You may need to consider one of the other alternative d(s): 196,211 WARNING @ Thu, 16 Apr 2020 00:30:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 16 Apr 2020 00:30:50: #3 Call peaks... INFO @ Thu, 16 Apr 2020 00:30:50: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 16 Apr 2020 00:30:57: #3 Call peaks for each chromosome... INFO @ Thu, 16 Apr 2020 00:31:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.10_peaks.xls INFO @ Thu, 16 Apr 2020 00:31:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.10_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:31:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.10_summits.bed INFO @ Thu, 16 Apr 2020 00:31:12: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (394 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Thu, 16 Apr 2020 00:31:22: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Thu, 16 Apr 2020 00:31:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.20_peaks.xls INFO @ Thu, 16 Apr 2020 00:31:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.20_peaks.narrowPeak INFO @ Thu, 16 Apr 2020 00:31:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6619538/SRX6619538.20_summits.bed INFO @ Thu, 16 Apr 2020 00:31:36: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (233 records, 4 fields): 1 millis CompletedMACS2peakCalling BigWig に変換しました。