[2023-03-17 05:26:45,846] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:26:45,846] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:26:45,847] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c6204b0-239b-4441-8bcd-fcb158f1f1b8/dqc_reference
[2023-03-17 05:26:46,943] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:26:46,943] [INFO] Task started: Prodigal
[2023-03-17 05:26:46,943] [INFO] Running command: cat /var/lib/cwl/stg27c74ffd-3711-42a1-92bb-c5582cf7d669/OceanDNA-b24525.fa | prodigal -d OceanDNA-b24525/cds.fna -a OceanDNA-b24525/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:26:51,434] [INFO] Task succeeded: Prodigal
[2023-03-17 05:26:51,435] [INFO] Task started: HMMsearch
[2023-03-17 05:26:51,435] [INFO] Running command: hmmsearch --tblout OceanDNA-b24525/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c6204b0-239b-4441-8bcd-fcb158f1f1b8/dqc_reference/reference_markers.hmm OceanDNA-b24525/protein.faa > /dev/null
[2023-03-17 05:26:51,580] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:26:51,581] [INFO] Found 6/6 markers.
[2023-03-17 05:26:51,589] [INFO] Query marker FASTA was written to OceanDNA-b24525/markers.fasta
[2023-03-17 05:26:51,589] [INFO] Task started: Blastn
[2023-03-17 05:26:51,589] [INFO] Running command: blastn -query OceanDNA-b24525/markers.fasta -db /var/lib/cwl/stg1c6204b0-239b-4441-8bcd-fcb158f1f1b8/dqc_reference/reference_markers.fasta -out OceanDNA-b24525/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:26:52,097] [INFO] Task succeeded: Blastn
[2023-03-17 05:26:52,098] [INFO] Selected 14 target genomes.
[2023-03-17 05:26:52,098] [INFO] Target genome list was writen to OceanDNA-b24525/target_genomes.txt
[2023-03-17 05:26:52,106] [INFO] Task started: fastANI
[2023-03-17 05:26:52,106] [INFO] Running command: fastANI --query /var/lib/cwl/stg27c74ffd-3711-42a1-92bb-c5582cf7d669/OceanDNA-b24525.fa --refList OceanDNA-b24525/target_genomes.txt --output OceanDNA-b24525/fastani_result.tsv --threads 1
[2023-03-17 05:26:57,962] [INFO] Task succeeded: fastANI
[2023-03-17 05:26:57,963] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c6204b0-239b-4441-8bcd-fcb158f1f1b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:26:57,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c6204b0-239b-4441-8bcd-fcb158f1f1b8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:26:57,963] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:26:57,963] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:26:57,963] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-03-17 05:26:57,963] [INFO] DFAST Taxonomy check result was written to OceanDNA-b24525/tc_result.tsv
[2023-03-17 05:26:57,963] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:26:57,963] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:26:57,963] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c6204b0-239b-4441-8bcd-fcb158f1f1b8/dqc_reference/checkm_data
[2023-03-17 05:26:57,966] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:26:57,969] [INFO] Task started: CheckM
[2023-03-17 05:26:57,969] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b24525/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b24525/checkm_input OceanDNA-b24525/checkm_result
[2023-03-17 05:27:15,325] [INFO] Task succeeded: CheckM
[2023-03-17 05:27:15,326] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 1.30%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:27:15,327] [INFO] ===== Completeness check finished =====
[2023-03-17 05:27:15,327] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:27:15,327] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b24525/markers.fasta)
[2023-03-17 05:27:15,328] [INFO] Task started: Blastn
[2023-03-17 05:27:15,328] [INFO] Running command: blastn -query OceanDNA-b24525/markers.fasta -db /var/lib/cwl/stg1c6204b0-239b-4441-8bcd-fcb158f1f1b8/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b24525/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:27:16,062] [INFO] Task succeeded: Blastn
[2023-03-17 05:27:16,063] [INFO] Selected 18 target genomes.
[2023-03-17 05:27:16,063] [INFO] Target genome list was writen to OceanDNA-b24525/target_genomes_gtdb.txt
[2023-03-17 05:27:16,377] [INFO] Task started: fastANI
[2023-03-17 05:27:16,377] [INFO] Running command: fastANI --query /var/lib/cwl/stg27c74ffd-3711-42a1-92bb-c5582cf7d669/OceanDNA-b24525.fa --refList OceanDNA-b24525/target_genomes_gtdb.txt --output OceanDNA-b24525/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:27:19,986] [INFO] Task succeeded: fastANI
[2023-03-17 05:27:19,995] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:27:19,995] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_002169365.1	s__HIMB59 sp002169365	96.9712	124	219	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004321805.1	s__HIMB59 sp004321805	83.1835	172	219	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902509695.1	s__HIMB59 sp902509695	79.0497	81	219	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902621205.1	s__HIMB59 sp902621205	78.4605	77	219	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.28	98.69	0.88	0.86	4	-
GCA_000299115.1	s__HIMB59 sp000299115	78.3839	113	219	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902599045.1	s__HIMB59 sp902615815	78.2202	85	219	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	96.41	95.18	0.86	0.81	23	-
GCA_008638215.1	s__HIMB59 sp008638215	78.1912	103	219	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.46	99.38	0.89	0.85	4	-
GCA_902610175.1	s__HIMB59 sp902610175	78.0749	94	219	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	96.44	96.34	0.91	0.90	4	-
GCA_902529795.1	s__HIMB59 sp902529795	77.664	65	219	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902601865.1	s__HIMB59 sp902601865	77.6224	86	219	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902528805.1	s__HIMB59 sp902528805	77.5676	54	219	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902599405.1	s__HIMB59 sp902599405	77.389	76	219	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.30	95.00	0.81	0.78	10	-
GCA_902538085.1	s__HIMB59 sp902538085	77.385	71	219	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	95.32	95.03	0.79	0.77	3	-
GCA_902588615.1	s__HIMB59 sp902588615	77.1471	68	219	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__HIMB59;f__HIMB59;g__HIMB59	95.0	99.82	99.82	0.73	0.73	2	-
--------------------------------------------------------------------------------
[2023-03-17 05:27:19,995] [INFO] GTDB search result was written to OceanDNA-b24525/result_gtdb.tsv
[2023-03-17 05:27:19,995] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:27:19,996] [INFO] DFAST_QC result json was written to OceanDNA-b24525/dqc_result.json
[2023-03-17 05:27:19,996] [INFO] DFAST_QC completed!
[2023-03-17 05:27:19,996] [INFO] Total running time: 0h0m34s