[2024-01-25 19:51:20,641] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:51:20,642] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:51:20,642] [INFO] DQC Reference Directory: /var/lib/cwl/stg12aea0d9-0dd4-4570-b3f8-bf745382431b/dqc_reference
[2024-01-25 19:51:21,858] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:51:21,858] [INFO] Task started: Prodigal
[2024-01-25 19:51:21,859] [INFO] Running command: gunzip -c /var/lib/cwl/stgaabab8bd-74e5-47c9-91da-92bf3aee2d79/GCF_016406085.1_ASM1640608v1_genomic.fna.gz | prodigal -d GCF_016406085.1_ASM1640608v1_genomic.fna/cds.fna -a GCF_016406085.1_ASM1640608v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:51:34,343] [INFO] Task succeeded: Prodigal
[2024-01-25 19:51:34,343] [INFO] Task started: HMMsearch
[2024-01-25 19:51:34,344] [INFO] Running command: hmmsearch --tblout GCF_016406085.1_ASM1640608v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12aea0d9-0dd4-4570-b3f8-bf745382431b/dqc_reference/reference_markers.hmm GCF_016406085.1_ASM1640608v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:51:34,653] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:51:34,654] [INFO] Found 6/6 markers.
[2024-01-25 19:51:34,690] [INFO] Query marker FASTA was written to GCF_016406085.1_ASM1640608v1_genomic.fna/markers.fasta
[2024-01-25 19:51:34,691] [INFO] Task started: Blastn
[2024-01-25 19:51:34,691] [INFO] Running command: blastn -query GCF_016406085.1_ASM1640608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12aea0d9-0dd4-4570-b3f8-bf745382431b/dqc_reference/reference_markers.fasta -out GCF_016406085.1_ASM1640608v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:35,331] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:35,334] [INFO] Selected 12 target genomes.
[2024-01-25 19:51:35,334] [INFO] Target genome list was writen to GCF_016406085.1_ASM1640608v1_genomic.fna/target_genomes.txt
[2024-01-25 19:51:35,340] [INFO] Task started: fastANI
[2024-01-25 19:51:35,340] [INFO] Running command: fastANI --query /var/lib/cwl/stgaabab8bd-74e5-47c9-91da-92bf3aee2d79/GCF_016406085.1_ASM1640608v1_genomic.fna.gz --refList GCF_016406085.1_ASM1640608v1_genomic.fna/target_genomes.txt --output GCF_016406085.1_ASM1640608v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:51:45,293] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:45,293] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12aea0d9-0dd4-4570-b3f8-bf745382431b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:51:45,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12aea0d9-0dd4-4570-b3f8-bf745382431b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:51:45,301] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:51:45,301] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:51:45,302] [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
Aureibaculum flavum	strain=A20	GCA_016406085.1	2795986	2795986	type	True	100.0	1568	1569	95	conclusive
Aureibaculum algae	strain=10Alg 115	GCA_006065315.1	2584122	2584122	type	True	92.3275	1289	1569	95	below_threshold
Aureibaculum luteum	strain=SM1352	GCA_003449015.1	1548456	1548456	type	True	92.1596	1313	1569	95	below_threshold
Aureibaculum marinum	strain=BH-SD17	GCA_003813905.1	2487930	2487930	type	True	80.0273	727	1569	95	below_threshold
Lutibacter maritimus	strain=DSM 24450	GCA_900116115.1	593133	593133	type	True	76.7308	206	1569	95	below_threshold
Polaribacter pectinis	strain=L12M9	GCA_014352875.1	2738844	2738844	type	True	76.618	211	1569	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	76.5859	168	1569	95	below_threshold
Polaribacter dokdonensis	strain=DSW-5	GCA_900106865.1	326329	326329	type	True	76.4514	185	1569	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	76.3471	110	1569	95	below_threshold
Flavobacterium lacus	strain=CGMCC 1.12504	GCA_003268815.1	1353778	1353778	type	True	76.2537	67	1569	95	below_threshold
Tenacibaculum ovolyticum	strain=DSM 18103	GCA_000430545.1	104270	104270	type	True	76.2458	172	1569	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	76.1219	108	1569	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:51:45,303] [INFO] DFAST Taxonomy check result was written to GCF_016406085.1_ASM1640608v1_genomic.fna/tc_result.tsv
[2024-01-25 19:51:45,303] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:51:45,303] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:51:45,304] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12aea0d9-0dd4-4570-b3f8-bf745382431b/dqc_reference/checkm_data
[2024-01-25 19:51:45,304] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:51:45,349] [INFO] Task started: CheckM
[2024-01-25 19:51:45,349] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016406085.1_ASM1640608v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016406085.1_ASM1640608v1_genomic.fna/checkm_input GCF_016406085.1_ASM1640608v1_genomic.fna/checkm_result
[2024-01-25 19:52:23,739] [INFO] Task succeeded: CheckM
[2024-01-25 19:52:23,740] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:52:23,763] [INFO] ===== Completeness check finished =====
[2024-01-25 19:52:23,763] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:52:23,764] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016406085.1_ASM1640608v1_genomic.fna/markers.fasta)
[2024-01-25 19:52:23,764] [INFO] Task started: Blastn
[2024-01-25 19:52:23,764] [INFO] Running command: blastn -query GCF_016406085.1_ASM1640608v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg12aea0d9-0dd4-4570-b3f8-bf745382431b/dqc_reference/reference_markers_gtdb.fasta -out GCF_016406085.1_ASM1640608v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:52:24,678] [INFO] Task succeeded: Blastn
[2024-01-25 19:52:24,681] [INFO] Selected 10 target genomes.
[2024-01-25 19:52:24,681] [INFO] Target genome list was writen to GCF_016406085.1_ASM1640608v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:52:24,694] [INFO] Task started: fastANI
[2024-01-25 19:52:24,694] [INFO] Running command: fastANI --query /var/lib/cwl/stgaabab8bd-74e5-47c9-91da-92bf3aee2d79/GCF_016406085.1_ASM1640608v1_genomic.fna.gz --refList GCF_016406085.1_ASM1640608v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016406085.1_ASM1640608v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:52:32,897] [INFO] Task succeeded: fastANI
[2024-01-25 19:52:32,904] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:52:32,904] [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_016406085.1	s__Aureibaculum sp016406085	100.0	1568	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_006065315.1	s__Aureibaculum sp006065315	92.3277	1289	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003449015.1	s__Aureibaculum sp003449015	92.1463	1314	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003813905.1	s__Aureibaculum marinum	80.0351	726	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002352665.1	s__Aureibaculum sp002352665	77.8899	383	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aureibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116115.1	s__Lutibacter maritimus	76.71	210	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310225.1	s__Algibacter_A alginicilyticus	76.5859	168	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013373105.1	s__Polaribacter sp013373105	76.5376	153	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001280865.1	s__Polaribacter dokdonensis	76.4969	182	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Polaribacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_004195315.1	s__Lutibacter sp004195315	76.3526	146	1569	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Lutibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:52:32,905] [INFO] GTDB search result was written to GCF_016406085.1_ASM1640608v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:52:32,905] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:52:32,908] [INFO] DFAST_QC result json was written to GCF_016406085.1_ASM1640608v1_genomic.fna/dqc_result.json
[2024-01-25 19:52:32,908] [INFO] DFAST_QC completed!
[2024-01-25 19:52:32,908] [INFO] Total running time: 0h1m12s