[2024-01-24 14:13:18,669] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:13:18,672] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:13:18,672] [INFO] DQC Reference Directory: /var/lib/cwl/stg60312785-bc13-44a6-b630-94003df3db37/dqc_reference
[2024-01-24 14:13:20,075] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:13:20,076] [INFO] Task started: Prodigal
[2024-01-24 14:13:20,076] [INFO] Running command: gunzip -c /var/lib/cwl/stg708bef3a-cfb7-4e1e-a6b3-376b3db85401/GCF_004349145.1_ASM434914v1_genomic.fna.gz | prodigal -d GCF_004349145.1_ASM434914v1_genomic.fna/cds.fna -a GCF_004349145.1_ASM434914v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:13:33,626] [INFO] Task succeeded: Prodigal
[2024-01-24 14:13:33,626] [INFO] Task started: HMMsearch
[2024-01-24 14:13:33,626] [INFO] Running command: hmmsearch --tblout GCF_004349145.1_ASM434914v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg60312785-bc13-44a6-b630-94003df3db37/dqc_reference/reference_markers.hmm GCF_004349145.1_ASM434914v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:13:33,896] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:13:33,902] [INFO] Found 6/6 markers.
[2024-01-24 14:13:33,934] [INFO] Query marker FASTA was written to GCF_004349145.1_ASM434914v1_genomic.fna/markers.fasta
[2024-01-24 14:13:33,935] [INFO] Task started: Blastn
[2024-01-24 14:13:33,935] [INFO] Running command: blastn -query GCF_004349145.1_ASM434914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60312785-bc13-44a6-b630-94003df3db37/dqc_reference/reference_markers.fasta -out GCF_004349145.1_ASM434914v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:34,630] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:34,637] [INFO] Selected 16 target genomes.
[2024-01-24 14:13:34,637] [INFO] Target genome list was writen to GCF_004349145.1_ASM434914v1_genomic.fna/target_genomes.txt
[2024-01-24 14:13:34,653] [INFO] Task started: fastANI
[2024-01-24 14:13:34,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg708bef3a-cfb7-4e1e-a6b3-376b3db85401/GCF_004349145.1_ASM434914v1_genomic.fna.gz --refList GCF_004349145.1_ASM434914v1_genomic.fna/target_genomes.txt --output GCF_004349145.1_ASM434914v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:49,454] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:49,455] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg60312785-bc13-44a6-b630-94003df3db37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:49,455] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg60312785-bc13-44a6-b630-94003df3db37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:49,468] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:13:49,469] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:13:49,469] [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
Flavobacterium hiemivividum	strain=TSA-D2	GCA_004349145.1	2541734	2541734	type	True	100.0	1229	1229	95	conclusive
Flavobacterium gillisiae	strain=DSM 22376	GCA_900107635.1	150146	150146	type	True	84.1339	833	1229	95	below_threshold
Flavobacterium frigoris	strain=DSM 15719	GCA_900111075.1	229204	229204	type	True	83.9808	800	1229	95	below_threshold
Flavobacterium degerlachei	strain=DSM 15718	GCA_900106645.1	229203	229203	type	True	80.7123	597	1229	95	below_threshold
Flavobacterium muglaense	strain=F-60	GCA_014305155.1	2764716	2764716	type	True	80.2057	509	1229	95	below_threshold
Flavobacterium xinjiangense	strain=CGMCC 1.2749	GCA_900142885.1	178356	178356	type	True	79.7411	510	1229	95	below_threshold
Flavobacterium urumqiense	strain=CGMCC 1.9230	GCA_900108015.1	935224	935224	type	True	79.7111	498	1229	95	below_threshold
Flavobacterium frigidarium	strain=DSM 17623	GCA_000425505.1	99286	99286	type	True	79.675	430	1229	95	below_threshold
Flavobacterium weaverense	strain=DSM 19727	GCA_003688495.1	271156	271156	type	True	79.5768	447	1229	95	below_threshold
Flavobacterium flabelliforme	strain=P4023	GCA_017948675.1	2816119	2816119	type	True	79.5747	492	1229	95	below_threshold
Flavobacterium gawalongense	strain=GSP16	GCA_007097265.1	2594432	2594432	type	True	79.4481	529	1229	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	78.6913	385	1229	95	below_threshold
Flavobacterium soyae	strain=SCIV07	GCA_021245985.1	2903098	2903098	type	True	78.241	354	1229	95	below_threshold
Flavobacterium tyrosinilyticum	strain=KCTC 42726	GCA_023656565.1	1658740	1658740	type	True	78.1079	360	1229	95	below_threshold
Flavobacterium endoglycinae	strain=BB8	GCA_017352115.1	2816357	2816357	type	True	78.0615	364	1229	95	below_threshold
Polaribacter dokdonensis	strain=KCTC 12392	GCA_024362345.1	326329	326329	type	True	76.21	78	1229	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:49,471] [INFO] DFAST Taxonomy check result was written to GCF_004349145.1_ASM434914v1_genomic.fna/tc_result.tsv
[2024-01-24 14:13:49,471] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:49,471] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:49,471] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg60312785-bc13-44a6-b630-94003df3db37/dqc_reference/checkm_data
[2024-01-24 14:13:49,472] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:49,513] [INFO] Task started: CheckM
[2024-01-24 14:13:49,513] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004349145.1_ASM434914v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004349145.1_ASM434914v1_genomic.fna/checkm_input GCF_004349145.1_ASM434914v1_genomic.fna/checkm_result
[2024-01-24 14:14:30,003] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:30,005] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:30,028] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:30,029] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:30,029] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004349145.1_ASM434914v1_genomic.fna/markers.fasta)
[2024-01-24 14:14:30,030] [INFO] Task started: Blastn
[2024-01-24 14:14:30,030] [INFO] Running command: blastn -query GCF_004349145.1_ASM434914v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg60312785-bc13-44a6-b630-94003df3db37/dqc_reference/reference_markers_gtdb.fasta -out GCF_004349145.1_ASM434914v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:30,950] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:30,954] [INFO] Selected 7 target genomes.
[2024-01-24 14:14:30,955] [INFO] Target genome list was writen to GCF_004349145.1_ASM434914v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:30,963] [INFO] Task started: fastANI
[2024-01-24 14:14:30,964] [INFO] Running command: fastANI --query /var/lib/cwl/stg708bef3a-cfb7-4e1e-a6b3-376b3db85401/GCF_004349145.1_ASM434914v1_genomic.fna.gz --refList GCF_004349145.1_ASM434914v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004349145.1_ASM434914v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:37,699] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:37,711] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:37,711] [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_004349145.1	s__Flavobacterium hiemivividum	100.0	1229	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	95.37	95.37	0.86	0.86	2	conclusive
GCF_900107635.1	s__Flavobacterium gillisiae	84.1747	829	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111075.1	s__Flavobacterium frigoris	83.9927	799	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002836475.1	s__Flavobacterium sp002836475	82.9963	713	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000264055.1	s__Flavobacterium sp000264055	82.1672	707	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900106645.1	s__Flavobacterium degerlachei	80.6999	599	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014281985.1	s__Flavobacterium sp014281985	79.6803	468	1229	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.07	98.07	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:37,713] [INFO] GTDB search result was written to GCF_004349145.1_ASM434914v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:37,714] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:37,717] [INFO] DFAST_QC result json was written to GCF_004349145.1_ASM434914v1_genomic.fna/dqc_result.json
[2024-01-24 14:14:37,717] [INFO] DFAST_QC completed!
[2024-01-24 14:14:37,717] [INFO] Total running time: 0h1m19s