[2024-01-24 13:58:55,297] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:55,299] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:55,299] [INFO] DQC Reference Directory: /var/lib/cwl/stg24ed878a-8840-47ce-8d4b-593b5612a9e7/dqc_reference
[2024-01-24 13:58:56,696] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:56,697] [INFO] Task started: Prodigal
[2024-01-24 13:58:56,697] [INFO] Running command: gunzip -c /var/lib/cwl/stgc8894650-d5f9-4c84-9b85-7cdab3af527f/GCF_011762485.1_ASM1176248v1_genomic.fna.gz | prodigal -d GCF_011762485.1_ASM1176248v1_genomic.fna/cds.fna -a GCF_011762485.1_ASM1176248v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:59:10,820] [INFO] Task succeeded: Prodigal
[2024-01-24 13:59:10,820] [INFO] Task started: HMMsearch
[2024-01-24 13:59:10,820] [INFO] Running command: hmmsearch --tblout GCF_011762485.1_ASM1176248v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24ed878a-8840-47ce-8d4b-593b5612a9e7/dqc_reference/reference_markers.hmm GCF_011762485.1_ASM1176248v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:59:11,053] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:59:11,055] [INFO] Found 6/6 markers.
[2024-01-24 13:59:11,090] [INFO] Query marker FASTA was written to GCF_011762485.1_ASM1176248v1_genomic.fna/markers.fasta
[2024-01-24 13:59:11,090] [INFO] Task started: Blastn
[2024-01-24 13:59:11,090] [INFO] Running command: blastn -query GCF_011762485.1_ASM1176248v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24ed878a-8840-47ce-8d4b-593b5612a9e7/dqc_reference/reference_markers.fasta -out GCF_011762485.1_ASM1176248v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:11,777] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:11,780] [INFO] Selected 19 target genomes.
[2024-01-24 13:59:11,780] [INFO] Target genome list was writen to GCF_011762485.1_ASM1176248v1_genomic.fna/target_genomes.txt
[2024-01-24 13:59:11,798] [INFO] Task started: fastANI
[2024-01-24 13:59:11,798] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8894650-d5f9-4c84-9b85-7cdab3af527f/GCF_011762485.1_ASM1176248v1_genomic.fna.gz --refList GCF_011762485.1_ASM1176248v1_genomic.fna/target_genomes.txt --output GCF_011762485.1_ASM1176248v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:25,049] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:25,050] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24ed878a-8840-47ce-8d4b-593b5612a9e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:25,050] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24ed878a-8840-47ce-8d4b-593b5612a9e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:25,065] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:59:25,065] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:25,065] [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
Yeosuana marina	strain=JLT21	GCA_011762485.1	1565536	1565536	type	True	100.0	1360	1362	95	conclusive
Yeosuana aromativorans	strain=JCM 12862	GCA_014646655.1	288019	288019	type	True	80.242	641	1362	95	below_threshold
Confluentibacter sediminis	strain=DSL-48	GCA_003258355.1	2219045	2219045	type	True	78.6484	437	1362	95	below_threshold
Confluentibacter lentus	strain=HJM-3	GCA_002806995.1	1699412	1699412	type	True	78.367	366	1362	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	78.0293	329	1362	95	below_threshold
Flavivirga rizhaonensis	strain=RZ03	GCA_004791695.1	2559571	2559571	type	True	77.9577	395	1362	95	below_threshold
Algibacter pectinivorans	strain=DSM 25730	GCA_900112595.1	870482	870482	type	True	77.8303	366	1362	95	below_threshold
Algibacter lectus	strain=DSM 15365	GCA_900112395.1	221126	221126	type	True	77.8223	338	1362	95	below_threshold
Algibacter alginicilyticus	strain=HZ22	GCA_001310225.1	1736674	1736674	type	True	77.8199	392	1362	95	below_threshold
Flavivirga algicola	strain=Y03	GCA_012910715.1	2729136	2729136	type	True	77.8186	380	1362	95	below_threshold
Arenitalea lutea	strain=P7-3-5	GCA_000283015.1	1178825	1178825	type	True	77.7756	375	1362	95	below_threshold
Arenitalea lutea	strain=CGMCC 1.12213	GCA_900141715.1	1178825	1178825	type	True	77.7718	370	1362	95	below_threshold
Changchengzhania lutea	strain=SM1355	GCA_006974145.1	2049305	2049305	type	True	77.6932	376	1362	95	below_threshold
Bizionia echini	strain=DSM 23925	GCA_900115185.1	649333	649333	type	True	77.6388	260	1362	95	below_threshold
Hanstruepera flava	strain=NBU2984	GCA_023634025.1	2930218	2930218	type	True	77.4732	241	1362	95	below_threshold
Hyunsoonleella ulvae	strain=HU1-3	GCA_016827605.1	2799948	2799948	type	True	77.3157	276	1362	95	below_threshold
Psychroserpens jangbogonensis	strain=PAMC 27130	GCA_000797465.1	1484460	1484460	type	True	77.2045	215	1362	95	below_threshold
Olleya marilimosa	strain=CAM030	GCA_000518485.1	272164	272164	type	True	77.0898	267	1362	95	below_threshold
Psychroserpens luteolus	strain=XSD401	GCA_021032705.1	2855840	2855840	type	True	76.9371	221	1362	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:25,067] [INFO] DFAST Taxonomy check result was written to GCF_011762485.1_ASM1176248v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:25,068] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:25,068] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:25,068] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24ed878a-8840-47ce-8d4b-593b5612a9e7/dqc_reference/checkm_data
[2024-01-24 13:59:25,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:25,112] [INFO] Task started: CheckM
[2024-01-24 13:59:25,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_011762485.1_ASM1176248v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_011762485.1_ASM1176248v1_genomic.fna/checkm_input GCF_011762485.1_ASM1176248v1_genomic.fna/checkm_result
[2024-01-24 14:00:05,267] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:05,269] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:05,288] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:05,288] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:05,289] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_011762485.1_ASM1176248v1_genomic.fna/markers.fasta)
[2024-01-24 14:00:05,289] [INFO] Task started: Blastn
[2024-01-24 14:00:05,289] [INFO] Running command: blastn -query GCF_011762485.1_ASM1176248v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24ed878a-8840-47ce-8d4b-593b5612a9e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_011762485.1_ASM1176248v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:06,269] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:06,272] [INFO] Selected 14 target genomes.
[2024-01-24 14:00:06,272] [INFO] Target genome list was writen to GCF_011762485.1_ASM1176248v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:06,294] [INFO] Task started: fastANI
[2024-01-24 14:00:06,294] [INFO] Running command: fastANI --query /var/lib/cwl/stgc8894650-d5f9-4c84-9b85-7cdab3af527f/GCF_011762485.1_ASM1176248v1_genomic.fna.gz --refList GCF_011762485.1_ASM1176248v1_genomic.fna/target_genomes_gtdb.txt --output GCF_011762485.1_ASM1176248v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:16,707] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:16,719] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:16,719] [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_011762485.1	s__Yeosuana marina	100.0	1360	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014646655.1	s__Yeosuana aromativorans	80.2696	635	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002441545.1	s__Yeosuana sp002441545	79.6522	582	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002784145.1	s__Yeosuana sp002784145	79.3928	515	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Yeosuana	95.0	99.75	99.57	0.88	0.85	11	-
GCA_003258355.1	s__Confluentibacter sp003258355	78.6375	437	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114265.1	s__Flaviramulus basaltis	78.483	502	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flaviramulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000789235.1	s__Wocania ichthyoenteri	78.4695	468	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Wocania	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002806995.1	s__Confluentibacter lentus	78.3522	368	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Confluentibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017814435.1	s__Mariniflexile gromovii	78.2751	410	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Mariniflexile	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004791695.1	s__Flavivirga rizhaonensis	77.9463	395	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavivirga	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001310225.1	s__Algibacter_A alginicilyticus	77.819	392	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Algibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610635.1	s__Ichthyenterobacterium magnum	77.8001	266	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ichthyenterobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006974145.1	s__Changchengzhania lutea	77.718	374	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Changchengzhania	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002162765.1	s__MAAR01 sp002162765	77.4043	201	1362	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__MAAR01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:16,721] [INFO] GTDB search result was written to GCF_011762485.1_ASM1176248v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:16,722] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:16,726] [INFO] DFAST_QC result json was written to GCF_011762485.1_ASM1176248v1_genomic.fna/dqc_result.json
[2024-01-24 14:00:16,726] [INFO] DFAST_QC completed!
[2024-01-24 14:00:16,726] [INFO] Total running time: 0h1m21s