[2023-03-15 21:01:44,312] [INFO] DFAST_QC pipeline started.
[2023-03-15 21:01:44,312] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 21:01:44,312] [INFO] DQC Reference Directory: /var/lib/cwl/stg3fbddf82-e405-4070-a7e1-921ece5c2cd4/dqc_reference
[2023-03-15 21:01:45,701] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 21:01:45,702] [INFO] Task started: Prodigal
[2023-03-15 21:01:45,702] [INFO] Running command: cat /var/lib/cwl/stg39e25842-8b94-432d-a081-f8325bef01e0/OceanDNA-b31211.fa | prodigal -d OceanDNA-b31211/cds.fna -a OceanDNA-b31211/protein.faa -g 11 -q > /dev/null
[2023-03-15 21:02:08,462] [INFO] Task succeeded: Prodigal
[2023-03-15 21:02:08,462] [INFO] Task started: HMMsearch
[2023-03-15 21:02:08,462] [INFO] Running command: hmmsearch --tblout OceanDNA-b31211/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3fbddf82-e405-4070-a7e1-921ece5c2cd4/dqc_reference/reference_markers.hmm OceanDNA-b31211/protein.faa > /dev/null
[2023-03-15 21:02:08,646] [INFO] Task succeeded: HMMsearch
[2023-03-15 21:02:08,647] [INFO] Found 6/6 markers.
[2023-03-15 21:02:08,671] [INFO] Query marker FASTA was written to OceanDNA-b31211/markers.fasta
[2023-03-15 21:02:08,671] [INFO] Task started: Blastn
[2023-03-15 21:02:08,671] [INFO] Running command: blastn -query OceanDNA-b31211/markers.fasta -db /var/lib/cwl/stg3fbddf82-e405-4070-a7e1-921ece5c2cd4/dqc_reference/reference_markers.fasta -out OceanDNA-b31211/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:02:09,240] [INFO] Task succeeded: Blastn
[2023-03-15 21:02:09,241] [INFO] Selected 26 target genomes.
[2023-03-15 21:02:09,241] [INFO] Target genome list was writen to OceanDNA-b31211/target_genomes.txt
[2023-03-15 21:02:09,256] [INFO] Task started: fastANI
[2023-03-15 21:02:09,256] [INFO] Running command: fastANI --query /var/lib/cwl/stg39e25842-8b94-432d-a081-f8325bef01e0/OceanDNA-b31211.fa --refList OceanDNA-b31211/target_genomes.txt --output OceanDNA-b31211/fastani_result.tsv --threads 1
[2023-03-15 21:02:27,354] [INFO] Task succeeded: fastANI
[2023-03-15 21:02:27,355] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3fbddf82-e405-4070-a7e1-921ece5c2cd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 21:02:27,355] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3fbddf82-e405-4070-a7e1-921ece5c2cd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 21:02:27,359] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 21:02:27,359] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-15 21:02:27,359] [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
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.5348	62	1145	95	below_threshold
Oceanibaculum indicum	strain=P24	GCA_000299935.1	526216	526216	type	True	75.4754	55	1145	95	below_threshold
Nisaea acidiphila	strain=MEBiC11861	GCA_024662015.1	1862145	1862145	type	True	75.3684	50	1145	95	below_threshold
Magnetospirillum kuznetsovii	strain=LBB-42	GCA_003284725.1	2053833	2053833	type	True	75.123	55	1145	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-15 21:02:27,359] [INFO] DFAST Taxonomy check result was written to OceanDNA-b31211/tc_result.tsv
[2023-03-15 21:02:27,360] [INFO] ===== Taxonomy check completed =====
[2023-03-15 21:02:27,360] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 21:02:27,360] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3fbddf82-e405-4070-a7e1-921ece5c2cd4/dqc_reference/checkm_data
[2023-03-15 21:02:27,360] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 21:02:27,366] [INFO] Task started: CheckM
[2023-03-15 21:02:27,366] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b31211/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b31211/checkm_input OceanDNA-b31211/checkm_result
[2023-03-15 21:03:24,927] [INFO] Task succeeded: CheckM
[2023-03-15 21:03:24,928] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 21:03:24,930] [INFO] ===== Completeness check finished =====
[2023-03-15 21:03:24,930] [INFO] ===== Start GTDB Search =====
[2023-03-15 21:03:24,931] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b31211/markers.fasta)
[2023-03-15 21:03:24,931] [INFO] Task started: Blastn
[2023-03-15 21:03:24,931] [INFO] Running command: blastn -query OceanDNA-b31211/markers.fasta -db /var/lib/cwl/stg3fbddf82-e405-4070-a7e1-921ece5c2cd4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b31211/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 21:03:25,779] [INFO] Task succeeded: Blastn
[2023-03-15 21:03:25,780] [INFO] Selected 24 target genomes.
[2023-03-15 21:03:25,780] [INFO] Target genome list was writen to OceanDNA-b31211/target_genomes_gtdb.txt
[2023-03-15 21:03:26,341] [INFO] Task started: fastANI
[2023-03-15 21:03:26,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg39e25842-8b94-432d-a081-f8325bef01e0/OceanDNA-b31211.fa --refList OceanDNA-b31211/target_genomes_gtdb.txt --output OceanDNA-b31211/fastani_result_gtdb.tsv --threads 1
[2023-03-15 21:03:43,281] [INFO] Task succeeded: fastANI
[2023-03-15 21:03:43,290] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 21:03:43,290] [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_018665815.1	s__UBA3470 sp018665815	99.7852	1061	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA3470	95.0	99.65	99.59	0.93	0.91	9	conclusive
GCA_002709525.1	s__UBA3470 sp002709525	77.0279	53	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA3470	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002378125.1	s__UBA3470 sp002378125	76.8749	87	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA3470	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018698795.1	s__TMED8 sp018698795	76.4514	117	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__TMED8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016845145.1	s__TMED8 sp016845145	76.3417	174	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__TMED8	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686255.1	s__Casp-alpha2 sp002686255	76.2372	88	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
GCA_014382345.1	s__Casp-alpha2 sp014382345	76.1594	87	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.86	99.86	0.92	0.92	2	-
GCA_002938075.1	s__Casp-alpha2 sp002938075	76.1368	64	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	98.70	98.63	0.78	0.77	3	-
GCA_002696205.1	s__UBA1479 sp002696205	76.1308	101	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002706405.1	s__UBA1479 sp002706405	76.0794	82	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__UBA1479	95.0	99.68	99.68	0.89	0.89	2	-
GCA_001510075.1	s__Casp-alpha2 sp001510075	76.0252	69	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859895.1	s__JACZKS01 sp014859895	75.7327	58	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__JAHDSF01;g__JACZKS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204265.1	s__Casp-alpha2 sp013204265	75.4796	62	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010725.1	s__Azospirillum lipoferum_B	75.2528	62	1145	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Azospirillales;f__Azospirillaceae;g__Azospirillum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 21:03:43,290] [INFO] GTDB search result was written to OceanDNA-b31211/result_gtdb.tsv
[2023-03-15 21:03:43,290] [INFO] ===== GTDB Search completed =====
[2023-03-15 21:03:43,291] [INFO] DFAST_QC result json was written to OceanDNA-b31211/dqc_result.json
[2023-03-15 21:03:43,291] [INFO] DFAST_QC completed!
[2023-03-15 21:03:43,291] [INFO] Total running time: 0h1m59s