[2023-03-16 12:37:45,678] [INFO] DFAST_QC pipeline started.
[2023-03-16 12:37:45,678] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 12:37:45,678] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb62687d-a89f-48b5-b51c-07c6c282825d/dqc_reference
[2023-03-16 12:37:47,957] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 12:37:47,957] [INFO] Task started: Prodigal
[2023-03-16 12:37:47,957] [INFO] Running command: cat /var/lib/cwl/stg9dbdda18-4f4b-4d1e-881e-f5a90d5b4555/OceanDNA-b38546.fa | prodigal -d OceanDNA-b38546/cds.fna -a OceanDNA-b38546/protein.faa -g 11 -q > /dev/null
[2023-03-16 12:38:05,616] [INFO] Task succeeded: Prodigal
[2023-03-16 12:38:05,616] [INFO] Task started: HMMsearch
[2023-03-16 12:38:05,616] [INFO] Running command: hmmsearch --tblout OceanDNA-b38546/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb62687d-a89f-48b5-b51c-07c6c282825d/dqc_reference/reference_markers.hmm OceanDNA-b38546/protein.faa > /dev/null
[2023-03-16 12:38:05,832] [INFO] Task succeeded: HMMsearch
[2023-03-16 12:38:05,833] [INFO] Found 6/6 markers.
[2023-03-16 12:38:05,849] [INFO] Query marker FASTA was written to OceanDNA-b38546/markers.fasta
[2023-03-16 12:38:05,850] [INFO] Task started: Blastn
[2023-03-16 12:38:05,850] [INFO] Running command: blastn -query OceanDNA-b38546/markers.fasta -db /var/lib/cwl/stgcb62687d-a89f-48b5-b51c-07c6c282825d/dqc_reference/reference_markers.fasta -out OceanDNA-b38546/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:38:06,489] [INFO] Task succeeded: Blastn
[2023-03-16 12:38:06,489] [INFO] Selected 18 target genomes.
[2023-03-16 12:38:06,490] [INFO] Target genome list was writen to OceanDNA-b38546/target_genomes.txt
[2023-03-16 12:38:06,501] [INFO] Task started: fastANI
[2023-03-16 12:38:06,501] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dbdda18-4f4b-4d1e-881e-f5a90d5b4555/OceanDNA-b38546.fa --refList OceanDNA-b38546/target_genomes.txt --output OceanDNA-b38546/fastani_result.tsv --threads 1
[2023-03-16 12:38:18,166] [INFO] Task succeeded: fastANI
[2023-03-16 12:38:18,167] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb62687d-a89f-48b5-b51c-07c6c282825d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 12:38:18,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb62687d-a89f-48b5-b51c-07c6c282825d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 12:38:18,178] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 12:38:18,178] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-03-16 12:38:18,178] [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
Acinetobacter bohemicus	strain=ANC 3994	GCA_000367925.1	1435036	1435036	type	True	83.5417	635	854	95	below_threshold
Acinetobacter terrae	strain=ANC 4282	GCA_013004375.1	2731247	2731247	type	True	83.157	588	854	95	below_threshold
Acinetobacter terrestris	strain=ANC 4471	GCA_004331155.1	2529843	2529843	suspected-type	True	82.6783	577	854	95	below_threshold
Acinetobacter albensis	strain=ANC 4874	GCA_900095025.1	1673609	1673609	type	True	82.2454	565	854	95	below_threshold
Acinetobacter harbinensis	strain=HITLi 7	GCA_000816495.1	1353941	1353941	type	True	81.1335	488	854	95	below_threshold
Acinetobacter silvestris	strain=ANC 4999	GCA_002135235.1	1977882	1977882	type	True	80.1646	439	854	95	below_threshold
Acinetobacter celticus	strain=ANC 4603	GCA_001707755.1	1891224	1891224	type	True	80.0932	456	854	95	below_threshold
Acinetobacter portensis	strain=AC 877	GCA_009372215.1	1839785	1839785	type	True	80.0642	413	854	95	below_threshold
Acinetobacter johnsonii	strain=DSM 6963	GCA_000949655.1	40214	40214	suspected-type	True	79.9828	426	854	95	below_threshold
Acinetobacter johnsonii	strain=NCTC10308	GCA_900444855.1	40214	40214	suspected-type	True	79.9804	439	854	95	below_threshold
Acinetobacter johnsonii	strain=CIP 64.6	GCA_000368045.1	40214	40214	suspected-type	True	79.9736	441	854	95	below_threshold
Acinetobacter johnsonii	strain=FDAARGOS_910	GCA_016027055.1	40214	40214	suspected-type	True	79.9587	453	854	95	below_threshold
Acinetobacter cumulans	strain=WCHAc060092	GCA_003024525.3	2136182	2136182	type	True	79.6008	395	854	95	below_threshold
Acinetobacter indicus	strain=DSM 25388	GCA_000830155.1	756892	756892	type	True	79.5161	337	854	95	below_threshold
Acinetobacter rongchengensis	strain=WCHAc060115	GCA_003611475.1	2419601	2419601	type	True	79.4819	406	854	95	below_threshold
Acinetobacter pecorum	strain=Sa1BUA6	GCA_014837015.1	2762215	2762215	type	True	79.1926	332	854	95	below_threshold
Acinetobacter junii	strain=NCTC10307	GCA_900444875.1	40215	40215	type	True	78.7555	286	854	95	below_threshold
Acinetobacter ihumii	strain=Marseille-P8049	GCA_900625095.1	2483802	2483802	type	True	78.7021	324	854	95	below_threshold
--------------------------------------------------------------------------------
[2023-03-16 12:38:18,178] [INFO] DFAST Taxonomy check result was written to OceanDNA-b38546/tc_result.tsv
[2023-03-16 12:38:18,178] [INFO] ===== Taxonomy check completed =====
[2023-03-16 12:38:18,178] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 12:38:18,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb62687d-a89f-48b5-b51c-07c6c282825d/dqc_reference/checkm_data
[2023-03-16 12:38:18,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 12:38:18,183] [INFO] Task started: CheckM
[2023-03-16 12:38:18,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b38546/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b38546/checkm_input OceanDNA-b38546/checkm_result
[2023-03-16 12:38:57,199] [INFO] Task succeeded: CheckM
[2023-03-16 12:38:57,199] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 69.59%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 12:38:57,202] [INFO] ===== Completeness check finished =====
[2023-03-16 12:38:57,202] [INFO] ===== Start GTDB Search =====
[2023-03-16 12:38:57,202] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b38546/markers.fasta)
[2023-03-16 12:38:57,203] [INFO] Task started: Blastn
[2023-03-16 12:38:57,203] [INFO] Running command: blastn -query OceanDNA-b38546/markers.fasta -db /var/lib/cwl/stgcb62687d-a89f-48b5-b51c-07c6c282825d/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b38546/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 12:38:58,198] [INFO] Task succeeded: Blastn
[2023-03-16 12:38:58,199] [INFO] Selected 16 target genomes.
[2023-03-16 12:38:58,199] [INFO] Target genome list was writen to OceanDNA-b38546/target_genomes_gtdb.txt
[2023-03-16 12:38:58,221] [INFO] Task started: fastANI
[2023-03-16 12:38:58,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg9dbdda18-4f4b-4d1e-881e-f5a90d5b4555/OceanDNA-b38546.fa --refList OceanDNA-b38546/target_genomes_gtdb.txt --output OceanDNA-b38546/fastani_result_gtdb.tsv --threads 1
[2023-03-16 12:39:11,881] [INFO] Task succeeded: fastANI
[2023-03-16 12:39:11,890] [INFO] Found 16 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 12:39:11,891] [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
GCF_002135335.1	s__Acinetobacter sp002135335	83.7471	584	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000367925.1	s__Acinetobacter bohemicus	83.5698	632	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.89	95.82	0.83	0.82	4	-
GCF_900107285.1	s__Acinetobacter kyonggiensis	83.5439	614	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.53	95.22	0.88	0.86	3	-
GCF_013004375.1	s__Acinetobacter terrae	83.1289	591	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.86	96.05	0.92	0.88	8	-
GCF_004336635.1	s__Acinetobacter sp004336635	82.9692	586	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	95.82	95.73	0.86	0.83	3	-
GCF_004331155.1	s__Acinetobacter terrestris	82.6986	577	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.13	95.48	0.90	0.88	5	-
GCF_004331285.1	s__Acinetobacter sp004331285	82.5862	588	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001647545.1	s__Acinetobacter sp001647545	82.3929	581	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.85	96.85	0.89	0.89	2	-
GCF_900095025.1	s__Acinetobacter albensis	82.2547	564	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	98.07	97.99	0.85	0.82	4	-
GCF_002135355.1	s__Acinetobacter sp002135355	81.5819	543	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902753875.1	s__Acinetobacter bouvetii_A	81.5395	522	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016599715.1	s__Acinetobacter sp002135245	81.1131	522	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.80	96.56	0.83	0.80	8	-
GCF_002135415.1	s__Acinetobacter sp002135415	80.1576	426	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002135345.1	s__Acinetobacter sp002135345	80.0874	410	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000368045.1	s__Acinetobacter johnsonii	79.9549	443	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	96.19	95.36	0.86	0.80	59	-
GCF_002165305.2	s__Acinetobacter sp002165305	79.9186	433	854	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Moraxellaceae;g__Acinetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 12:39:11,891] [INFO] GTDB search result was written to OceanDNA-b38546/result_gtdb.tsv
[2023-03-16 12:39:11,893] [INFO] ===== GTDB Search completed =====
[2023-03-16 12:39:11,895] [INFO] DFAST_QC result json was written to OceanDNA-b38546/dqc_result.json
[2023-03-16 12:39:11,896] [INFO] DFAST_QC completed!
[2023-03-16 12:39:11,896] [INFO] Total running time: 0h1m26s