[2024-01-24 14:11:50,853] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:50,856] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:50,857] [INFO] DQC Reference Directory: /var/lib/cwl/stg2074d3d0-afc3-4c5d-88e6-ebe494fd8540/dqc_reference
[2024-01-24 14:11:52,253] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:52,254] [INFO] Task started: Prodigal
[2024-01-24 14:11:52,255] [INFO] Running command: gunzip -c /var/lib/cwl/stg0e180ad5-9b6f-4e70-877c-36d250cd79a0/GCF_009846745.1_ASM984674v1_genomic.fna.gz | prodigal -d GCF_009846745.1_ASM984674v1_genomic.fna/cds.fna -a GCF_009846745.1_ASM984674v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:08,193] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:08,194] [INFO] Task started: HMMsearch
[2024-01-24 14:12:08,194] [INFO] Running command: hmmsearch --tblout GCF_009846745.1_ASM984674v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2074d3d0-afc3-4c5d-88e6-ebe494fd8540/dqc_reference/reference_markers.hmm GCF_009846745.1_ASM984674v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:08,589] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:08,590] [INFO] Found 6/6 markers.
[2024-01-24 14:12:08,634] [INFO] Query marker FASTA was written to GCF_009846745.1_ASM984674v1_genomic.fna/markers.fasta
[2024-01-24 14:12:08,634] [INFO] Task started: Blastn
[2024-01-24 14:12:08,634] [INFO] Running command: blastn -query GCF_009846745.1_ASM984674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2074d3d0-afc3-4c5d-88e6-ebe494fd8540/dqc_reference/reference_markers.fasta -out GCF_009846745.1_ASM984674v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:09,720] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:09,723] [INFO] Selected 11 target genomes.
[2024-01-24 14:12:09,724] [INFO] Target genome list was writen to GCF_009846745.1_ASM984674v1_genomic.fna/target_genomes.txt
[2024-01-24 14:12:09,731] [INFO] Task started: fastANI
[2024-01-24 14:12:09,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e180ad5-9b6f-4e70-877c-36d250cd79a0/GCF_009846745.1_ASM984674v1_genomic.fna.gz --refList GCF_009846745.1_ASM984674v1_genomic.fna/target_genomes.txt --output GCF_009846745.1_ASM984674v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:20,938] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:20,939] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2074d3d0-afc3-4c5d-88e6-ebe494fd8540/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:20,939] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2074d3d0-afc3-4c5d-88e6-ebe494fd8540/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:20,995] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:12:20,996] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:12:20,996] [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
Alcanivorax xenomutans	strain=JC109	GCA_900217905.1	1094342	1094342	type	True	91.6339	1277	1530	95	below_threshold
Alcanivorax dieselolei	strain=CGMCC 1.3690	GCA_014644575.1	285091	285091	type	True	90.5079	1303	1530	95	below_threshold
Alcanivorax balearicus	strain=MACL04	GCA_025532145.1	413232	413232	type	True	90.4852	1278	1530	95	below_threshold
Alcanivorax dieselolei	strain=B5	GCA_000300005.1	285091	285091	type	True	90.4695	1322	1530	95	below_threshold
Alcanivorax profundimaris	strain=ST75FaO-1	GCA_015265435.1	2735259	2735259	type	True	80.9281	701	1530	95	below_threshold
Alcanivorax marinus	strain=R8-12	GCA_025532125.1	1177169	1177169	type	True	80.9036	645	1530	95	below_threshold
Alcanivorax gelatiniphagus	strain=MEBiC 08158	GCA_005938655.1	1194167	1194167	type	True	80.6034	714	1530	95	below_threshold
Alcanivorax limicola	strain=JB21	GCA_019931215.1	2874102	2874102	type	True	77.6438	226	1530	95	below_threshold
Pseudomonas aromaticivorans	strain=MAP12	GCA_019097855.1	2849492	2849492	type	True	77.0204	157	1530	95	below_threshold
Pseudomonas cavernae	strain=K2W31S-8	GCA_003595175.1	2320867	2320867	type	True	76.5819	167	1530	95	below_threshold
Acidihalobacter aeolianus	strain=V6	GCA_001753165.1	2792603	2792603	type	True	75.4878	56	1530	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:20,997] [INFO] DFAST Taxonomy check result was written to GCF_009846745.1_ASM984674v1_genomic.fna/tc_result.tsv
[2024-01-24 14:12:20,998] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:20,998] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:20,999] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2074d3d0-afc3-4c5d-88e6-ebe494fd8540/dqc_reference/checkm_data
[2024-01-24 14:12:21,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:21,058] [INFO] Task started: CheckM
[2024-01-24 14:12:21,058] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009846745.1_ASM984674v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009846745.1_ASM984674v1_genomic.fna/checkm_input GCF_009846745.1_ASM984674v1_genomic.fna/checkm_result
[2024-01-24 14:13:07,864] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:07,866] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:07,886] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:07,887] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:07,887] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009846745.1_ASM984674v1_genomic.fna/markers.fasta)
[2024-01-24 14:13:07,888] [INFO] Task started: Blastn
[2024-01-24 14:13:07,888] [INFO] Running command: blastn -query GCF_009846745.1_ASM984674v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2074d3d0-afc3-4c5d-88e6-ebe494fd8540/dqc_reference/reference_markers_gtdb.fasta -out GCF_009846745.1_ASM984674v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:09,514] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:09,517] [INFO] Selected 10 target genomes.
[2024-01-24 14:13:09,517] [INFO] Target genome list was writen to GCF_009846745.1_ASM984674v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:09,525] [INFO] Task started: fastANI
[2024-01-24 14:13:09,525] [INFO] Running command: fastANI --query /var/lib/cwl/stg0e180ad5-9b6f-4e70-877c-36d250cd79a0/GCF_009846745.1_ASM984674v1_genomic.fna.gz --refList GCF_009846745.1_ASM984674v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009846745.1_ASM984674v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:13:19,456] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:19,488] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:13:19,488] [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_004360225.1	s__Alcanivorax sp004360225	99.1197	1388	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	99.14	99.14	0.91	0.91	2	conclusive
GCF_900217905.1	s__Alcanivorax xenomutans	91.6339	1277	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.43	98.18	0.92	0.84	9	-
GCF_000300005.1	s__Alcanivorax dieselolei	90.4695	1322	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.56	95.12	0.92	0.84	3	-
GCF_015265435.1	s__Alcanivorax profundimaris	80.9402	700	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.49	97.23	0.85	0.77	11	-
GCF_015356855.1	s__Alcanivorax venustensis	80.8705	619	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	97.73	95.38	0.91	0.87	46	-
GCF_016906305.1	s__Alcanivorax marinus_B	80.7334	700	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005938655.1	s__Alcanivorax gelatiniphagus	80.5998	716	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	98.53	98.53	0.93	0.93	3	-
GCF_016785095.1	s__Alcanivorax marinus_A	80.2811	691	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Alcanivoracaceae;g__Alcanivorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013391415.1	s__Aquitalea sp013391415	75.9484	70	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chromobacteriaceae;g__Aquitalea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001753165.1	s__Acidihalobacter aeolianus	75.5078	55	1530	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Ectothiorhodospirales;f__Acidihalobacteraceae;g__Acidihalobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:13:19,490] [INFO] GTDB search result was written to GCF_009846745.1_ASM984674v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:13:19,491] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:13:19,497] [INFO] DFAST_QC result json was written to GCF_009846745.1_ASM984674v1_genomic.fna/dqc_result.json
[2024-01-24 14:13:19,497] [INFO] DFAST_QC completed!
[2024-01-24 14:13:19,497] [INFO] Total running time: 0h1m29s