[2024-01-24 11:44:38,163] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:38,165] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:38,166] [INFO] DQC Reference Directory: /var/lib/cwl/stg47ba136e-a12f-4b9f-9ba4-1ef58049ed12/dqc_reference
[2024-01-24 11:44:41,489] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:41,490] [INFO] Task started: Prodigal
[2024-01-24 11:44:41,490] [INFO] Running command: gunzip -c /var/lib/cwl/stg906b9450-6733-49a2-a3c5-d82dab58ee26/GCF_030409805.1_ASM3040980v1_genomic.fna.gz | prodigal -d GCF_030409805.1_ASM3040980v1_genomic.fna/cds.fna -a GCF_030409805.1_ASM3040980v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:56,965] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:56,966] [INFO] Task started: HMMsearch
[2024-01-24 11:44:56,966] [INFO] Running command: hmmsearch --tblout GCF_030409805.1_ASM3040980v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47ba136e-a12f-4b9f-9ba4-1ef58049ed12/dqc_reference/reference_markers.hmm GCF_030409805.1_ASM3040980v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:57,258] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:57,259] [INFO] Found 6/6 markers.
[2024-01-24 11:44:57,301] [INFO] Query marker FASTA was written to GCF_030409805.1_ASM3040980v1_genomic.fna/markers.fasta
[2024-01-24 11:44:57,301] [INFO] Task started: Blastn
[2024-01-24 11:44:57,302] [INFO] Running command: blastn -query GCF_030409805.1_ASM3040980v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47ba136e-a12f-4b9f-9ba4-1ef58049ed12/dqc_reference/reference_markers.fasta -out GCF_030409805.1_ASM3040980v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:58,003] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:58,006] [INFO] Selected 13 target genomes.
[2024-01-24 11:44:58,007] [INFO] Target genome list was writen to GCF_030409805.1_ASM3040980v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:58,011] [INFO] Task started: fastANI
[2024-01-24 11:44:58,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg906b9450-6733-49a2-a3c5-d82dab58ee26/GCF_030409805.1_ASM3040980v1_genomic.fna.gz --refList GCF_030409805.1_ASM3040980v1_genomic.fna/target_genomes.txt --output GCF_030409805.1_ASM3040980v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:07,714] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:07,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47ba136e-a12f-4b9f-9ba4-1ef58049ed12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:07,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47ba136e-a12f-4b9f-9ba4-1ef58049ed12/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:07,728] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:45:07,728] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:45:07,728] [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
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	84.8859	957	1633	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	81.4705	702	1633	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	79.9337	600	1633	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	79.9043	600	1633	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	79.8938	602	1633	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	79.1747	529	1633	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	78.4991	422	1633	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	78.4751	429	1633	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	78.1178	359	1633	95	below_threshold
Lacinutrix mariniflava	strain=AKS432	GCA_001418015.1	342955	342955	type	True	77.9332	348	1633	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.5092	298	1633	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.451	305	1633	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	77.3899	277	1633	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:07,730] [INFO] DFAST Taxonomy check result was written to GCF_030409805.1_ASM3040980v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:07,730] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:07,730] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:07,731] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47ba136e-a12f-4b9f-9ba4-1ef58049ed12/dqc_reference/checkm_data
[2024-01-24 11:45:07,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:07,775] [INFO] Task started: CheckM
[2024-01-24 11:45:07,776] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409805.1_ASM3040980v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409805.1_ASM3040980v1_genomic.fna/checkm_input GCF_030409805.1_ASM3040980v1_genomic.fna/checkm_result
[2024-01-24 11:45:53,626] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:53,627] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:53,648] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:53,648] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:53,648] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409805.1_ASM3040980v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:53,649] [INFO] Task started: Blastn
[2024-01-24 11:45:53,652] [INFO] Running command: blastn -query GCF_030409805.1_ASM3040980v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg47ba136e-a12f-4b9f-9ba4-1ef58049ed12/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409805.1_ASM3040980v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:54,618] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:54,623] [INFO] Selected 9 target genomes.
[2024-01-24 11:45:54,624] [INFO] Target genome list was writen to GCF_030409805.1_ASM3040980v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:54,632] [INFO] Task started: fastANI
[2024-01-24 11:45:54,632] [INFO] Running command: fastANI --query /var/lib/cwl/stg906b9450-6733-49a2-a3c5-d82dab58ee26/GCF_030409805.1_ASM3040980v1_genomic.fna.gz --refList GCF_030409805.1_ASM3040980v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409805.1_ASM3040980v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:03,405] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:03,417] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 11:46:03,418] [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_900112395.1	s__Algibacter lectus	84.8684	959	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	98.81	98.79	0.90	0.89	6	-
GCF_009796825.1	s__Algibacter sp009796825	84.7179	998	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009796805.1	s__Algibacter sp009796805	82.4813	917	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033385.1	s__Algibacter pacificus	81.4751	701	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	79.9135	602	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	100.00	100.00	1.00	1.00	3	-
GCF_900112595.1	s__Algibacter_B pectinivorans	79.1871	527	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015355625.1	s__Tamlana_A sp015355625	78.8931	481	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	78.6222	468	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001418015.1	s__Lacinutrix mariniflava	77.9332	348	1633	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lacinutrix	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:46:03,419] [INFO] GTDB search result was written to GCF_030409805.1_ASM3040980v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:03,420] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:03,424] [INFO] DFAST_QC result json was written to GCF_030409805.1_ASM3040980v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:03,424] [INFO] DFAST_QC completed!
[2024-01-24 11:46:03,424] [INFO] Total running time: 0h1m25s