Job ID = 5790796 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2020-04-21T22:30:03 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 ) 2020-04-21T22:30:03 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 ) 2020-04-21T22:30:03 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 ) 2020-04-21T22:30:03 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 : 17,185,644 reads read : 34,371,288 reads written : 17,185,644 reads 0-length : 17,185,644 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:56 17185644 reads; of these: 17185644 (100.00%) were unpaired; of these: 6044402 (35.17%) aligned 0 times 8227589 (47.87%) aligned exactly 1 time 2913653 (16.95%) aligned >1 times 64.83% overall alignment rate Time searching: 00:10:57 Overall time: 00:10:57 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 895691 / 11141242 = 0.0804 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 07:46:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.bam'] # control file = None # effective genome size = 2.15e+09 # 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 07:46:00: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:46:00: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:46:08: 1000000 INFO @ Wed, 22 Apr 2020 07:46:16: 2000000 INFO @ Wed, 22 Apr 2020 07:46:24: 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 07:46:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.bam'] # control file = None # effective genome size = 2.15e+09 # 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 07:46:30: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:46:30: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:46:32: 4000000 INFO @ Wed, 22 Apr 2020 07:46:39: 1000000 INFO @ Wed, 22 Apr 2020 07:46:41: 5000000 INFO @ Wed, 22 Apr 2020 07:46:48: 2000000 INFO @ Wed, 22 Apr 2020 07:46:50: 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 @ Wed, 22 Apr 2020 07:46:57: 3000000 INFO @ Wed, 22 Apr 2020 07:46:58: 7000000 INFO @ Wed, 22 Apr 2020 07:46:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.bam'] # control file = None # effective genome size = 2.15e+09 # 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 07:46:59: #1 read tag files... INFO @ Wed, 22 Apr 2020 07:46:59: #1 read treatment tags... INFO @ Wed, 22 Apr 2020 07:47:06: 4000000 INFO @ Wed, 22 Apr 2020 07:47:07: 8000000 INFO @ Wed, 22 Apr 2020 07:47:08: 1000000 INFO @ Wed, 22 Apr 2020 07:47:15: 5000000 INFO @ Wed, 22 Apr 2020 07:47:16: 9000000 INFO @ Wed, 22 Apr 2020 07:47:17: 2000000 INFO @ Wed, 22 Apr 2020 07:47:23: 6000000 INFO @ Wed, 22 Apr 2020 07:47:25: 10000000 INFO @ Wed, 22 Apr 2020 07:47:26: 3000000 INFO @ Wed, 22 Apr 2020 07:47:27: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:47:27: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:47:27: #1 total tags in treatment: 10245551 INFO @ Wed, 22 Apr 2020 07:47:27: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:47:27: #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 07:47:27: #1 tags after filtering in treatment: 10245330 INFO @ Wed, 22 Apr 2020 07:47:27: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:47:27: #1 finished! INFO @ Wed, 22 Apr 2020 07:47:27: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:47:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:47:29: #2 number of paired peaks: 4973 INFO @ Wed, 22 Apr 2020 07:47:29: start model_add_line... INFO @ Wed, 22 Apr 2020 07:47:29: start X-correlation... INFO @ Wed, 22 Apr 2020 07:47:29: end of X-cor INFO @ Wed, 22 Apr 2020 07:47:29: #2 finished! INFO @ Wed, 22 Apr 2020 07:47:29: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 07:47:29: #2 alternative fragment length(s) may be 74,226,563 bps INFO @ Wed, 22 Apr 2020 07:47:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.05_model.r WARNING @ Wed, 22 Apr 2020 07:47:29: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:47:29: #2 You may need to consider one of the other alternative d(s): 74,226,563 WARNING @ Wed, 22 Apr 2020 07:47:29: #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 07:47:29: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:47:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:47:32: 7000000 INFO @ Wed, 22 Apr 2020 07:47:35: 4000000 INFO @ Wed, 22 Apr 2020 07:47:41: 8000000 INFO @ Wed, 22 Apr 2020 07:47:44: 5000000 INFO @ Wed, 22 Apr 2020 07:47:50: 9000000 INFO @ Wed, 22 Apr 2020 07:47:52: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:47:52: 6000000 INFO @ Wed, 22 Apr 2020 07:47:59: 10000000 INFO @ Wed, 22 Apr 2020 07:48:01: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:48:01: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:48:01: #1 total tags in treatment: 10245551 INFO @ Wed, 22 Apr 2020 07:48:01: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:48:01: #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 07:48:01: 7000000 INFO @ Wed, 22 Apr 2020 07:48:01: #1 tags after filtering in treatment: 10245330 INFO @ Wed, 22 Apr 2020 07:48:01: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:48:01: #1 finished! INFO @ Wed, 22 Apr 2020 07:48:01: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:48:01: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:48:03: #2 number of paired peaks: 4973 INFO @ Wed, 22 Apr 2020 07:48:03: start model_add_line... INFO @ Wed, 22 Apr 2020 07:48:03: start X-correlation... INFO @ Wed, 22 Apr 2020 07:48:03: end of X-cor INFO @ Wed, 22 Apr 2020 07:48:03: #2 finished! INFO @ Wed, 22 Apr 2020 07:48:03: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 07:48:03: #2 alternative fragment length(s) may be 74,226,563 bps INFO @ Wed, 22 Apr 2020 07:48:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.10_model.r WARNING @ Wed, 22 Apr 2020 07:48:03: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:48:03: #2 You may need to consider one of the other alternative d(s): 74,226,563 WARNING @ Wed, 22 Apr 2020 07:48:03: #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 07:48:03: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:48:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:48:03: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.05_peaks.xls INFO @ Wed, 22 Apr 2020 07:48:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.05_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:48:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.05_summits.bed INFO @ Wed, 22 Apr 2020 07:48:03: Done! pass1 - making usageList (66 chroms): 1 millis pass2 - checking and writing primary data (905 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 22 Apr 2020 07:48:09: 8000000 INFO @ Wed, 22 Apr 2020 07:48:17: 9000000 INFO @ Wed, 22 Apr 2020 07:48:25: 10000000 INFO @ Wed, 22 Apr 2020 07:48:26: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:48:27: #1 tag size is determined as 74 bps INFO @ Wed, 22 Apr 2020 07:48:27: #1 tag size = 74 INFO @ Wed, 22 Apr 2020 07:48:27: #1 total tags in treatment: 10245551 INFO @ Wed, 22 Apr 2020 07:48:27: #1 user defined the maximum tags... INFO @ Wed, 22 Apr 2020 07:48:27: #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 07:48:28: #1 tags after filtering in treatment: 10245330 INFO @ Wed, 22 Apr 2020 07:48:28: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 22 Apr 2020 07:48:28: #1 finished! INFO @ Wed, 22 Apr 2020 07:48:28: #2 Build Peak Model... INFO @ Wed, 22 Apr 2020 07:48:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 22 Apr 2020 07:48:29: #2 number of paired peaks: 4973 INFO @ Wed, 22 Apr 2020 07:48:29: start model_add_line... INFO @ Wed, 22 Apr 2020 07:48:29: start X-correlation... INFO @ Wed, 22 Apr 2020 07:48:29: end of X-cor INFO @ Wed, 22 Apr 2020 07:48:29: #2 finished! INFO @ Wed, 22 Apr 2020 07:48:29: #2 predicted fragment length is 74 bps INFO @ Wed, 22 Apr 2020 07:48:29: #2 alternative fragment length(s) may be 74,226,563 bps INFO @ Wed, 22 Apr 2020 07:48:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.20_model.r WARNING @ Wed, 22 Apr 2020 07:48:29: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 22 Apr 2020 07:48:29: #2 You may need to consider one of the other alternative d(s): 74,226,563 WARNING @ Wed, 22 Apr 2020 07:48:29: #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 07:48:29: #3 Call peaks... INFO @ Wed, 22 Apr 2020 07:48:29: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 22 Apr 2020 07:48:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.10_peaks.xls INFO @ Wed, 22 Apr 2020 07:48:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.10_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:48:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.10_summits.bed INFO @ Wed, 22 Apr 2020 07:48:37: Done! pass1 - making usageList (56 chroms): 1 millis pass2 - checking and writing primary data (537 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Wed, 22 Apr 2020 07:48:53: #3 Call peaks for each chromosome... INFO @ Wed, 22 Apr 2020 07:49:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.20_peaks.xls INFO @ Wed, 22 Apr 2020 07:49:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.20_peaks.narrowPeak INFO @ Wed, 22 Apr 2020 07:49:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX7625162/SRX7625162.20_summits.bed INFO @ Wed, 22 Apr 2020 07:49:05: Done! pass1 - making usageList (46 chroms): 0 millis pass2 - checking and writing primary data (292 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。