[2024-01-24 13:13:24,989] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:24,997] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:24,997] [INFO] DQC Reference Directory: /var/lib/cwl/stg08111b2f-eb9c-4e63-874b-b0590e363f04/dqc_reference
[2024-01-24 13:13:26,342] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:26,343] [INFO] Task started: Prodigal
[2024-01-24 13:13:26,343] [INFO] Running command: gunzip -c /var/lib/cwl/stg417729a8-1305-474c-b611-011312d618d4/GCF_004104035.1_ASM410403v1_genomic.fna.gz | prodigal -d GCF_004104035.1_ASM410403v1_genomic.fna/cds.fna -a GCF_004104035.1_ASM410403v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:43,581] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:43,581] [INFO] Task started: HMMsearch
[2024-01-24 13:13:43,582] [INFO] Running command: hmmsearch --tblout GCF_004104035.1_ASM410403v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08111b2f-eb9c-4e63-874b-b0590e363f04/dqc_reference/reference_markers.hmm GCF_004104035.1_ASM410403v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:43,915] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:43,916] [INFO] Found 6/6 markers.
[2024-01-24 13:13:43,983] [INFO] Query marker FASTA was written to GCF_004104035.1_ASM410403v1_genomic.fna/markers.fasta
[2024-01-24 13:13:43,984] [INFO] Task started: Blastn
[2024-01-24 13:13:43,984] [INFO] Running command: blastn -query GCF_004104035.1_ASM410403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08111b2f-eb9c-4e63-874b-b0590e363f04/dqc_reference/reference_markers.fasta -out GCF_004104035.1_ASM410403v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:44,698] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:44,702] [INFO] Selected 11 target genomes.
[2024-01-24 13:13:44,703] [INFO] Target genome list was writen to GCF_004104035.1_ASM410403v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:44,713] [INFO] Task started: fastANI
[2024-01-24 13:13:44,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg417729a8-1305-474c-b611-011312d618d4/GCF_004104035.1_ASM410403v1_genomic.fna.gz --refList GCF_004104035.1_ASM410403v1_genomic.fna/target_genomes.txt --output GCF_004104035.1_ASM410403v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:55,153] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:55,154] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08111b2f-eb9c-4e63-874b-b0590e363f04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:55,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08111b2f-eb9c-4e63-874b-b0590e363f04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:55,170] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:55,171] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:55,171] [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
Leeuwenhoekiella marinoflava	strain=LMG 1345	GCA_004104035.1	988	988	type	True	100.0	1555	1559	95	conclusive
Leeuwenhoekiella marinoflava	strain=DSM 3653	GCA_900129005.1	988	988	type	True	99.9931	1548	1559	95	conclusive
Leeuwenhoekiella aestuarii	strain=R-48165	GCA_004104055.1	2249426	2249426	type	True	86.439	1079	1559	95	below_threshold
Leeuwenhoekiella palythoae	strain=DSM 19859	GCA_900130045.1	573501	573501	type	True	80.3684	703	1559	95	below_threshold
Leeuwenhoekiella palythoae	strain=LMG 24856	GCA_004104045.1	573501	573501	type	True	80.2943	693	1559	95	below_threshold
Leeuwenhoekiella blandensis	strain=MED217	GCA_000152985.1	360293	360293	type	True	80.0953	729	1559	95	below_threshold
Algibacter pacificus	strain=H164	GCA_008033385.1	2599389	2599389	type	True	76.9553	93	1559	95	below_threshold
Hyunsoonleella flava	strain=T58	GCA_004310325.1	2527939	2527939	type	True	76.9239	82	1559	95	below_threshold
Aestuariivivens marinum	strain=MT3-5-12	GCA_022662175.1	2913555	2913555	type	True	76.3947	67	1559	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	76.0529	75	1559	95	below_threshold
Tenacibaculum todarodis	strain=LPB0136	GCA_001889045.1	1850252	1850252	type	True	75.8455	88	1559	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:55,173] [INFO] DFAST Taxonomy check result was written to GCF_004104035.1_ASM410403v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:55,174] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:55,174] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:55,174] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08111b2f-eb9c-4e63-874b-b0590e363f04/dqc_reference/checkm_data
[2024-01-24 13:13:55,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:55,222] [INFO] Task started: CheckM
[2024-01-24 13:13:55,222] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004104035.1_ASM410403v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004104035.1_ASM410403v1_genomic.fna/checkm_input GCF_004104035.1_ASM410403v1_genomic.fna/checkm_result
[2024-01-24 13:14:45,646] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:45,647] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:45,671] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:45,671] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:45,672] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004104035.1_ASM410403v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:45,672] [INFO] Task started: Blastn
[2024-01-24 13:14:45,672] [INFO] Running command: blastn -query GCF_004104035.1_ASM410403v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08111b2f-eb9c-4e63-874b-b0590e363f04/dqc_reference/reference_markers_gtdb.fasta -out GCF_004104035.1_ASM410403v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:46,648] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:46,652] [INFO] Selected 6 target genomes.
[2024-01-24 13:14:46,652] [INFO] Target genome list was writen to GCF_004104035.1_ASM410403v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:46,680] [INFO] Task started: fastANI
[2024-01-24 13:14:46,680] [INFO] Running command: fastANI --query /var/lib/cwl/stg417729a8-1305-474c-b611-011312d618d4/GCF_004104035.1_ASM410403v1_genomic.fna.gz --refList GCF_004104035.1_ASM410403v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004104035.1_ASM410403v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:54,130] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:54,137] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:54,137] [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_900129005.1	s__Leeuwenhoekiella marinoflava	99.9931	1548	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_004104075.1	s__Leeuwenhoekiella polynyae	87.3543	1136	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004104055.1	s__Leeuwenhoekiella aestuarii	86.4387	1079	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	99.75	99.75	0.97	0.97	2	-
GCF_900130045.1	s__Leeuwenhoekiella palythoae	80.3858	702	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	96.69	96.09	0.92	0.86	9	-
GCF_000152985.1	s__Leeuwenhoekiella blandensis	80.09	728	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	97.86	97.58	0.89	0.73	11	-
GCF_000687915.1	s__Leeuwenhoekiella sp000687915	79.7006	601	1559	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Leeuwenhoekiella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:54,139] [INFO] GTDB search result was written to GCF_004104035.1_ASM410403v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:54,139] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:54,142] [INFO] DFAST_QC result json was written to GCF_004104035.1_ASM410403v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:54,142] [INFO] DFAST_QC completed!
[2024-01-24 13:14:54,142] [INFO] Total running time: 0h1m29s