Job ID = 5790991 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... 2020-04-21T23:07:15 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - mbedtls_ssl_handshake returned -76 ( NET - Reading information from the socket failed ) 2020-04-21T23:07:15 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - ktls_handshake failed while accessing '165.112.9.235' from '172.19.7.198' 2020-04-21T23:07:15 fasterq-dump.2.9.6 sys: connection failed while opening file within cryptographic module - Failed to create TLS stream for 'sra-download.ncbi.nlm.nih.gov' (165.112.9.235) from '172.19.7.198' 2020-04-21T23:07:15 fasterq-dump.2.9.6 err: connection failed while opening file within cryptographic module - error with https open 'https://sra-download.ncbi.nlm.nih.gov/traces/sra42/SRR/008886/SRR9099527' 2020-04-21T23:07:15 fasterq-dump.2.9.6 err: invalid accession 'SRR9099527' spots read : 3,334,185 reads read : 6,668,370 reads written : 6,668,370 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: 00:02:42 3334185 reads; of these: 3334185 (100.00%) were paired; of these: 176407 (5.29%) aligned concordantly 0 times 2459992 (73.78%) aligned concordantly exactly 1 time 697786 (20.93%) aligned concordantly >1 times ---- 176407 pairs aligned concordantly 0 times; of these: 1116 (0.63%) aligned discordantly 1 time ---- 175291 pairs aligned 0 times concordantly or discordantly; of these: 350582 mates make up the pairs; of these: 326272 (93.07%) aligned 0 times 16332 (4.66%) aligned exactly 1 time 7978 (2.28%) aligned >1 times 95.11% overall alignment rate Time searching: 00:02:42 Overall time: 00:02:42 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] 42017 / 3140980 = 0.0134 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 08:17:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.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 08:17:13: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:17:13: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:17:20: 1000000 INFO @ Wed, 22 Apr 2020 08:17:27: 2000000 INFO @ Wed, 22 Apr 2020 08:17:34: 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 @ Wed, 22 Apr 2020 08:17:40: 4000000 INFO @ Wed, 22 Apr 2020 08:17:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.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 08:17:44: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:17:44: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:17:47: 5000000 INFO @ Wed, 22 Apr 2020 08:17:50: 1000000 INFO @ Wed, 22 Apr 2020 08:17:55: 6000000 INFO @ Wed, 22 Apr 2020 08:17:56: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:17:56: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:17:56: #1 total tags in treatment: 3115762 INFO @ Wed, 22 Apr 2020 08:17:56: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:17:56: #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 08:17:57: #1 tags after filtering in treatment: 2637944 INFO @ Wed, 22 Apr 2020 08:17:57: #1 Redundant rate of treatment: 0.15 INFO @ Wed, 22 Apr 2020 08:17:57: #1 finished! INFO @ Wed, 22 Apr 2020 08:17:57: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:17:57: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:17:57: 2000000 INFO @ Wed, 22 Apr 2020 08:17:57: #2 number of paired peaks: 213 WARNING @ Wed, 22 Apr 2020 08:17:57: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Wed, 22 Apr 2020 08:17:57: start model_add_line... INFO @ Wed, 22 Apr 2020 08:17:57: start X-correlation... INFO @ Wed, 22 Apr 2020 08:17:57: end of X-cor INFO @ Wed, 22 Apr 2020 08:17:57: #2 finished! INFO @ Wed, 22 Apr 2020 08:17:57: #2 predicted fragment length is 131 bps INFO @ Wed, 22 Apr 2020 08:17:57: #2 alternative fragment length(s) may be 2,109,131 bps INFO @ Wed, 22 Apr 2020 08:17:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.05_model.r WARNING @ Wed, 22 Apr 2020 08:17:57: #2 Since the d (131) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:17:57: #2 You may need to consider one of the other alternative d(s): 2,109,131 WARNING @ Wed, 22 Apr 2020 08:17:57: #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 08:17:57: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:17:57: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:18:03: 3000000 INFO @ Wed, 22 Apr 2020 08:18:03: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:18:05: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.05_peaks.xls INFO @ Wed, 22 Apr 2020 08:18:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:18:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.05_summits.bed INFO @ Wed, 22 Apr 2020 08:18:05: Done! INFO @ Wed, 22 Apr 2020 08:18:09: 4000000 pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (491 records, 4 fields): 2 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 08:18:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.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 08:18:14: #1 read tag files... INFO @ Wed, 22 Apr 2020 08:18:14: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 08:18:15: 5000000 INFO @ Wed, 22 Apr 2020 08:18:21: 6000000 INFO @ Wed, 22 Apr 2020 08:18:22: 1000000 INFO @ Wed, 22 Apr 2020 08:18:23: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:18:23: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:18:23: #1 total tags in treatment: 3115762 INFO @ Wed, 22 Apr 2020 08:18:23: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:18:23: #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 08:18:23: #1 tags after filtering in treatment: 2637944 INFO @ Wed, 22 Apr 2020 08:18:23: #1 Redundant rate of treatment: 0.15 INFO @ Wed, 22 Apr 2020 08:18:23: #1 finished! INFO @ Wed, 22 Apr 2020 08:18:23: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:18:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:18:23: #2 number of paired peaks: 213 WARNING @ Wed, 22 Apr 2020 08:18:23: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Wed, 22 Apr 2020 08:18:23: start model_add_line... INFO @ Wed, 22 Apr 2020 08:18:23: start X-correlation... INFO @ Wed, 22 Apr 2020 08:18:23: end of X-cor INFO @ Wed, 22 Apr 2020 08:18:23: #2 finished! INFO @ Wed, 22 Apr 2020 08:18:23: #2 predicted fragment length is 131 bps INFO @ Wed, 22 Apr 2020 08:18:23: #2 alternative fragment length(s) may be 2,109,131 bps INFO @ Wed, 22 Apr 2020 08:18:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.10_model.r WARNING @ Wed, 22 Apr 2020 08:18:23: #2 Since the d (131) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:18:23: #2 You may need to consider one of the other alternative d(s): 2,109,131 WARNING @ Wed, 22 Apr 2020 08:18:23: #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 08:18:23: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:18:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:18:29: 2000000 INFO @ Wed, 22 Apr 2020 08:18:29: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 08:18:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.10_peaks.xls INFO @ Wed, 22 Apr 2020 08:18:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:18:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.10_summits.bed INFO @ Wed, 22 Apr 2020 08:18:31: Done! pass1 - making usageList (17 chroms): 3 millis pass2 - checking and writing primary data (311 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 08:18:36: 3000000 INFO @ Wed, 22 Apr 2020 08:18:43: 4000000 INFO @ Wed, 22 Apr 2020 08:18:49: 5000000 INFO @ Wed, 22 Apr 2020 08:18:56: 6000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 08:18:58: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 08:18:58: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 08:18:58: #1 total tags in treatment: 3115762 INFO @ Wed, 22 Apr 2020 08:18:58: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 08:18:58: #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 08:18:58: #1 tags after filtering in treatment: 2637944 INFO @ Wed, 22 Apr 2020 08:18:58: #1 Redundant rate of treatment: 0.15 INFO @ Wed, 22 Apr 2020 08:18:58: #1 finished! INFO @ Wed, 22 Apr 2020 08:18:58: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 08:18:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 08:18:58: #2 number of paired peaks: 213 WARNING @ Wed, 22 Apr 2020 08:18:58: Fewer paired peaks (213) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 213 pairs to build model! INFO @ Wed, 22 Apr 2020 08:18:58: start model_add_line... INFO @ Wed, 22 Apr 2020 08:18:58: start X-correlation... INFO @ Wed, 22 Apr 2020 08:18:58: end of X-cor INFO @ Wed, 22 Apr 2020 08:18:58: #2 finished! INFO @ Wed, 22 Apr 2020 08:18:58: #2 predicted fragment length is 131 bps INFO @ Wed, 22 Apr 2020 08:18:58: #2 alternative fragment length(s) may be 2,109,131 bps INFO @ Wed, 22 Apr 2020 08:18:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.20_model.r WARNING @ Wed, 22 Apr 2020 08:18:58: #2 Since the d (131) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 08:18:58: #2 You may need to consider one of the other alternative d(s): 2,109,131 WARNING @ Wed, 22 Apr 2020 08:18:58: #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 08:18:58: #3 Call peaks... INFO @ Wed, 22 Apr 2020 08:18:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 08:19:05: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Wed, 22 Apr 2020 08:19:07: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.20_peaks.xls INFO @ Wed, 22 Apr 2020 08:19:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 08:19:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX5874490/SRX5874490.20_summits.bed INFO @ Wed, 22 Apr 2020 08:19:07: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (132 records, 4 fields): 1 millis CompletedMACS2peakCalling