[2024-01-24 11:44:38,170] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:38,171] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:38,171] [INFO] DQC Reference Directory: /var/lib/cwl/stg03b8a9f6-9914-4699-a4e7-3ec9915fb91a/dqc_reference
[2024-01-24 11:44:41,487] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:41,488] [INFO] Task started: Prodigal
[2024-01-24 11:44:41,488] [INFO] Running command: gunzip -c /var/lib/cwl/stg12d4d9e5-8f57-4c37-8ccb-82c0d2d0370a/GCF_016428595.1_ASM1642859v1_genomic.fna.gz | prodigal -d GCF_016428595.1_ASM1642859v1_genomic.fna/cds.fna -a GCF_016428595.1_ASM1642859v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:56,906] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:56,907] [INFO] Task started: HMMsearch
[2024-01-24 11:44:56,907] [INFO] Running command: hmmsearch --tblout GCF_016428595.1_ASM1642859v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg03b8a9f6-9914-4699-a4e7-3ec9915fb91a/dqc_reference/reference_markers.hmm GCF_016428595.1_ASM1642859v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:57,179] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:57,181] [INFO] Found 6/6 markers.
[2024-01-24 11:44:57,220] [INFO] Query marker FASTA was written to GCF_016428595.1_ASM1642859v1_genomic.fna/markers.fasta
[2024-01-24 11:44:57,221] [INFO] Task started: Blastn
[2024-01-24 11:44:57,221] [INFO] Running command: blastn -query GCF_016428595.1_ASM1642859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03b8a9f6-9914-4699-a4e7-3ec9915fb91a/dqc_reference/reference_markers.fasta -out GCF_016428595.1_ASM1642859v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:57,895] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:57,899] [INFO] Selected 20 target genomes.
[2024-01-24 11:44:57,900] [INFO] Target genome list was writen to GCF_016428595.1_ASM1642859v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:57,930] [INFO] Task started: fastANI
[2024-01-24 11:44:57,931] [INFO] Running command: fastANI --query /var/lib/cwl/stg12d4d9e5-8f57-4c37-8ccb-82c0d2d0370a/GCF_016428595.1_ASM1642859v1_genomic.fna.gz --refList GCF_016428595.1_ASM1642859v1_genomic.fna/target_genomes.txt --output GCF_016428595.1_ASM1642859v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:45:12,127] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:12,128] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg03b8a9f6-9914-4699-a4e7-3ec9915fb91a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:45:12,129] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg03b8a9f6-9914-4699-a4e7-3ec9915fb91a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:45:12,151] [INFO] Found 20 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:45:12,151] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:45:12,152] [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
Snuella sedimenti	strain=CAU 1569	GCA_016428595.1	2798802	2798802	type	True	100.0	1425	1430	95	conclusive
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	78.2009	326	1430	95	below_threshold
Changchengzhania lutea	strain=SM1355	GCA_006974145.1	2049305	2049305	type	True	77.9572	252	1430	95	below_threshold
Flavivirga eckloniae	strain=ECD14	GCA_002886045.1	1803846	1803846	type	True	77.9296	316	1430	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.8534	326	1430	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	77.8285	281	1430	95	below_threshold
Mariniflexile fucanivorans	strain=DSM 18792	GCA_004341235.1	264023	264023	type	True	77.7747	317	1430	95	below_threshold
Algibacter onchidii	strain=XY-114	GCA_004804355.1	2562860	2562860	type	True	77.7608	232	1430	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.7108	356	1430	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_008630605.1	1608400	1608400	type	True	77.6896	285	1430	95	below_threshold
Algibacter amylolyticus	strain=RU-4-M-4	GCA_007559325.1	1608400	1608400	type	True	77.6896	285	1430	95	below_threshold
Algibacter amylolyticus	strain=DSM 29199	GCA_014202225.1	1608400	1608400	type	True	77.6666	289	1430	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	77.5919	209	1430	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	77.5067	255	1430	95	below_threshold
Hanstruepera marina	strain=NBU2968	GCA_019880635.1	2873265	2873265	type	True	77.4883	184	1430	95	below_threshold
Yeosuana aromativorans	strain=JCM 12862	GCA_014646655.1	288019	288019	type	True	77.4421	252	1430	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.2913	224	1430	95	below_threshold
Xanthomarina gelatinilytica	strain=AK20	GCA_000348685.1	1137281	1137281	type	True	77.0993	175	1430	95	below_threshold
Oceanihabitans sediminis	strain=S9-10	GCA_003337215.1	1812012	1812012	type	True	77.0709	169	1430	95	below_threshold
Oceanihabitans sediminis	strain=DSM 28133	GCA_003315315.1	1812012	1812012	type	True	77.0517	175	1430	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:45:12,154] [INFO] DFAST Taxonomy check result was written to GCF_016428595.1_ASM1642859v1_genomic.fna/tc_result.tsv
[2024-01-24 11:45:12,154] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:45:12,155] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:45:12,155] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg03b8a9f6-9914-4699-a4e7-3ec9915fb91a/dqc_reference/checkm_data
[2024-01-24 11:45:12,156] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:45:12,211] [INFO] Task started: CheckM
[2024-01-24 11:45:12,212] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016428595.1_ASM1642859v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016428595.1_ASM1642859v1_genomic.fna/checkm_input GCF_016428595.1_ASM1642859v1_genomic.fna/checkm_result
[2024-01-24 11:45:57,700] [INFO] Task succeeded: CheckM
[2024-01-24 11:45:57,701] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:45:57,720] [INFO] ===== Completeness check finished =====
[2024-01-24 11:45:57,721] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:45:57,721] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016428595.1_ASM1642859v1_genomic.fna/markers.fasta)
[2024-01-24 11:45:57,722] [INFO] Task started: Blastn
[2024-01-24 11:45:57,722] [INFO] Running command: blastn -query GCF_016428595.1_ASM1642859v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg03b8a9f6-9914-4699-a4e7-3ec9915fb91a/dqc_reference/reference_markers_gtdb.fasta -out GCF_016428595.1_ASM1642859v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:45:58,618] [INFO] Task succeeded: Blastn
[2024-01-24 11:45:58,623] [INFO] Selected 18 target genomes.
[2024-01-24 11:45:58,623] [INFO] Target genome list was writen to GCF_016428595.1_ASM1642859v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:45:58,635] [INFO] Task started: fastANI
[2024-01-24 11:45:58,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg12d4d9e5-8f57-4c37-8ccb-82c0d2d0370a/GCF_016428595.1_ASM1642859v1_genomic.fna.gz --refList GCF_016428595.1_ASM1642859v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016428595.1_ASM1642859v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:46:11,807] [INFO] Task succeeded: fastANI
[2024-01-24 11:46:11,835] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:46:11,835] [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_016428595.1	s__Snuella sp016428595	100.0	1425	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Snuella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000789235.1	s__Wocania ichthyoenteri	78.5224	371	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	78.1165	320	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006974145.1	s__Changchengzhania lutea	77.971	251	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Changchengzhania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013001275.1	s__Flaviramulus sp013001275	77.9413	231	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002886045.1	s__Flavivirga eckloniae	77.9261	317	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001747085.1	s__Algibacter_C aquaticus	77.889	310	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012910715.1	s__Flavivirga sp012910715	77.8511	327	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341235.1	s__Mariniflexile fucanivorans	77.7845	316	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004804355.1	s__Tamlana_C sp004804355	77.7416	232	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Tamlana_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	77.7096	357	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202225.1	s__Algibacter_B amylolyticus	77.6559	290	1430	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_004310325.1	s__Jejuia sp004310325	77.5919	209	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997385.1	s__Seonamhaeicola algicola	77.4583	256	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Seonamhaeicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016827605.1	s__Jejuia sp016827605	77.3025	223	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002973595.1	s__Jejuia pallidilutea	77.1134	261	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Jejuia	95.0	98.03	97.97	0.83	0.83	4	-
GCF_003337215.1	s__Oceanihabitans sediminis	77.0865	168	1430	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Oceanihabitans	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001874145.1	s__Lacinutrix sp001874145	76.9519	180	1430	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 11:46:11,837] [INFO] GTDB search result was written to GCF_016428595.1_ASM1642859v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:46:11,837] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:46:11,842] [INFO] DFAST_QC result json was written to GCF_016428595.1_ASM1642859v1_genomic.fna/dqc_result.json
[2024-01-24 11:46:11,842] [INFO] DFAST_QC completed!
[2024-01-24 11:46:11,842] [INFO] Total running time: 0h1m34s