Job ID = 5791235 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-22T00:12:31 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 : 4,000,000 reads read : 8,000,000 reads written : 8,000,000 2020-04-22T00:16:09 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 ) 2020-04-22T00:16:09 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 ) 2020-04-22T00:16:10 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 ) 2020-04-22T00:17:06 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 : 990,307 reads read : 1,980,614 reads written : 1,980,614 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: 00:02:31 4990307 reads; of these: 4990307 (100.00%) were paired; of these: 3429585 (68.72%) aligned concordantly 0 times 1138753 (22.82%) aligned concordantly exactly 1 time 421969 (8.46%) aligned concordantly >1 times ---- 3429585 pairs aligned concordantly 0 times; of these: 31765 (0.93%) aligned discordantly 1 time ---- 3397820 pairs aligned 0 times concordantly or discordantly; of these: 6795640 mates make up the pairs; of these: 6706028 (98.68%) aligned 0 times 46951 (0.69%) aligned exactly 1 time 42661 (0.63%) aligned >1 times 32.81% overall alignment rate Time searching: 00:02:31 Overall time: 00:02:31 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [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 chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 983781 / 1589387 = 0.6190 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 @ Wed, 22 Apr 2020 09:22:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.bam'] # control file = None # effective genome size = 1.21e+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, 22 Apr 2020 09:22:19: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:22:19: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:22:24: 1000000 INFO @ Wed, 22 Apr 2020 09:22:26: #1 tag size is determined as 125 bps INFO @ Wed, 22 Apr 2020 09:22:26: #1 tag size = 125 INFO @ Wed, 22 Apr 2020 09:22:26: #1 total tags in treatment: 592408 INFO @ Wed, 22 Apr 2020 09:22:26: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:22:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 09:22:26: #1 tags after filtering in treatment: 385218 INFO @ Wed, 22 Apr 2020 09:22:26: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 22 Apr 2020 09:22:26: #1 finished! INFO @ Wed, 22 Apr 2020 09:22:26: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:22:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:22:26: #2 number of paired peaks: 516 WARNING @ Wed, 22 Apr 2020 09:22:26: Fewer paired peaks (516) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 516 pairs to build model! INFO @ Wed, 22 Apr 2020 09:22:26: start model_add_line... INFO @ Wed, 22 Apr 2020 09:22:26: start X-correlation... INFO @ Wed, 22 Apr 2020 09:22:26: end of X-cor INFO @ Wed, 22 Apr 2020 09:22:26: #2 finished! INFO @ Wed, 22 Apr 2020 09:22:26: #2 predicted fragment length is 223 bps INFO @ Wed, 22 Apr 2020 09:22:26: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 22 Apr 2020 09:22:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.05_model.r WARNING @ Wed, 22 Apr 2020 09:22:26: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 09:22:26: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 22 Apr 2020 09:22:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 09:22:26: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:22:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:22:28: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:22:29: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.05_peaks.xls INFO @ Wed, 22 Apr 2020 09:22:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:22:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.05_summits.bed INFO @ Wed, 22 Apr 2020 09:22:29: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (571 records, 4 fields): 2 millis CompletedMACS2peakCalling 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 @ Wed, 22 Apr 2020 09:22:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.bam'] # control file = None # effective genome size = 1.21e+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, 22 Apr 2020 09:22:49: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:22:49: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:22:54: 1000000 INFO @ Wed, 22 Apr 2020 09:22:56: #1 tag size is determined as 125 bps INFO @ Wed, 22 Apr 2020 09:22:56: #1 tag size = 125 INFO @ Wed, 22 Apr 2020 09:22:56: #1 total tags in treatment: 592408 INFO @ Wed, 22 Apr 2020 09:22:56: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:22:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 09:22:56: #1 tags after filtering in treatment: 385218 INFO @ Wed, 22 Apr 2020 09:22:56: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 22 Apr 2020 09:22:56: #1 finished! INFO @ Wed, 22 Apr 2020 09:22:56: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:22:56: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:22:56: #2 number of paired peaks: 516 WARNING @ Wed, 22 Apr 2020 09:22:56: Fewer paired peaks (516) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 516 pairs to build model! INFO @ Wed, 22 Apr 2020 09:22:56: start model_add_line... INFO @ Wed, 22 Apr 2020 09:22:56: start X-correlation... INFO @ Wed, 22 Apr 2020 09:22:56: end of X-cor INFO @ Wed, 22 Apr 2020 09:22:56: #2 finished! INFO @ Wed, 22 Apr 2020 09:22:56: #2 predicted fragment length is 223 bps INFO @ Wed, 22 Apr 2020 09:22:56: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 22 Apr 2020 09:22:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.10_model.r WARNING @ Wed, 22 Apr 2020 09:22:56: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 09:22:56: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 22 Apr 2020 09:22:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 09:22:56: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:22:56: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 09:22:58: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:22:58: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.10_peaks.xls INFO @ Wed, 22 Apr 2020 09:22:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:22:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.10_summits.bed INFO @ Wed, 22 Apr 2020 09:22:58: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (471 records, 4 fields): 3 millis CompletedMACS2peakCalling 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 @ Wed, 22 Apr 2020 09:23:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.bam'] # control file = None # effective genome size = 1.21e+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, 22 Apr 2020 09:23:19: #1 read tag files... INFO @ Wed, 22 Apr 2020 09:23:19: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 09:23:25: 1000000 INFO @ Wed, 22 Apr 2020 09:23:27: #1 tag size is determined as 125 bps INFO @ Wed, 22 Apr 2020 09:23:27: #1 tag size = 125 INFO @ Wed, 22 Apr 2020 09:23:27: #1 total tags in treatment: 592408 INFO @ Wed, 22 Apr 2020 09:23:27: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 09:23:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 22 Apr 2020 09:23:27: #1 tags after filtering in treatment: 385218 INFO @ Wed, 22 Apr 2020 09:23:27: #1 Redundant rate of treatment: 0.35 INFO @ Wed, 22 Apr 2020 09:23:27: #1 finished! INFO @ Wed, 22 Apr 2020 09:23:27: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 09:23:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 09:23:27: #2 number of paired peaks: 516 WARNING @ Wed, 22 Apr 2020 09:23:27: Fewer paired peaks (516) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 516 pairs to build model! INFO @ Wed, 22 Apr 2020 09:23:27: start model_add_line... INFO @ Wed, 22 Apr 2020 09:23:27: start X-correlation... INFO @ Wed, 22 Apr 2020 09:23:27: end of X-cor INFO @ Wed, 22 Apr 2020 09:23:27: #2 finished! INFO @ Wed, 22 Apr 2020 09:23:27: #2 predicted fragment length is 223 bps INFO @ Wed, 22 Apr 2020 09:23:27: #2 alternative fragment length(s) may be 223 bps INFO @ Wed, 22 Apr 2020 09:23:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.20_model.r WARNING @ Wed, 22 Apr 2020 09:23:27: #2 Since the d (223) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 09:23:27: #2 You may need to consider one of the other alternative d(s): 223 WARNING @ Wed, 22 Apr 2020 09:23:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 22 Apr 2020 09:23:27: #3 Call peaks... INFO @ Wed, 22 Apr 2020 09:23:27: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 09:23:29: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 09:23:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.20_peaks.xls INFO @ Wed, 22 Apr 2020 09:23:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 09:23:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX7256001/SRX7256001.20_summits.bed INFO @ Wed, 22 Apr 2020 09:23:30: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (340 records, 4 fields): 1 millis CompletedMACS2peakCalling