[2024-01-25 18:03:05,743] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:03:05,744] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:03:05,745] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b864a80-0b24-4442-a50f-b90d02996ba7/dqc_reference
[2024-01-25 18:03:06,898] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:03:06,899] [INFO] Task started: Prodigal
[2024-01-25 18:03:06,899] [INFO] Running command: gunzip -c /var/lib/cwl/stg7e4c299b-4d7e-4e7f-975d-309636eeef49/GCF_000620145.1_ASM62014v1_genomic.fna.gz | prodigal -d GCF_000620145.1_ASM62014v1_genomic.fna/cds.fna -a GCF_000620145.1_ASM62014v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:03:16,213] [INFO] Task succeeded: Prodigal
[2024-01-25 18:03:16,213] [INFO] Task started: HMMsearch
[2024-01-25 18:03:16,213] [INFO] Running command: hmmsearch --tblout GCF_000620145.1_ASM62014v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b864a80-0b24-4442-a50f-b90d02996ba7/dqc_reference/reference_markers.hmm GCF_000620145.1_ASM62014v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:03:16,427] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:03:16,429] [INFO] Found 6/6 markers.
[2024-01-25 18:03:16,459] [INFO] Query marker FASTA was written to GCF_000620145.1_ASM62014v1_genomic.fna/markers.fasta
[2024-01-25 18:03:16,459] [INFO] Task started: Blastn
[2024-01-25 18:03:16,459] [INFO] Running command: blastn -query GCF_000620145.1_ASM62014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b864a80-0b24-4442-a50f-b90d02996ba7/dqc_reference/reference_markers.fasta -out GCF_000620145.1_ASM62014v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:17,087] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:17,089] [INFO] Selected 14 target genomes.
[2024-01-25 18:03:17,090] [INFO] Target genome list was writen to GCF_000620145.1_ASM62014v1_genomic.fna/target_genomes.txt
[2024-01-25 18:03:17,101] [INFO] Task started: fastANI
[2024-01-25 18:03:17,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e4c299b-4d7e-4e7f-975d-309636eeef49/GCF_000620145.1_ASM62014v1_genomic.fna.gz --refList GCF_000620145.1_ASM62014v1_genomic.fna/target_genomes.txt --output GCF_000620145.1_ASM62014v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:03:26,637] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:26,637] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b864a80-0b24-4442-a50f-b90d02996ba7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:03:26,638] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b864a80-0b24-4442-a50f-b90d02996ba7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:03:26,644] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:03:26,644] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:03:26,644] [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
Deefgea rivuli	strain=DSM 18356	GCA_000620145.1	400948	400948	type	True	100.0	1226	1227	95	conclusive
Deefgea chitinilytica	strain=LMG 24817	GCA_016881405.1	570276	570276	type	True	81.2	690	1227	95	below_threshold
Deefgea salmonis	strain=H3-26	GCA_020531905.1	2875502	2875502	type	True	80.6087	588	1227	95	below_threshold
Chitinibacter bivalviorum	strain=2T18	GCA_013403565.1	2739434	2739434	type	True	78.273	370	1227	95	below_threshold
Chitinibacter fontanus	strain=STM-7	GCA_013423785.1	1737446	1737446	type	True	78.0745	355	1227	95	below_threshold
Chitinibacter tainanensis	strain=DSM 15459	GCA_000429785.1	230667	230667	type	True	77.4713	297	1227	95	below_threshold
Iodobacter ciconiae	strain=H11R3	GCA_003952345.1	2496266	2496266	type	True	76.844	148	1227	95	below_threshold
Iodobacter fluviatilis	strain=NCTC11159	GCA_900451195.1	537	537	type	True	76.6235	174	1227	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:03:26,646] [INFO] DFAST Taxonomy check result was written to GCF_000620145.1_ASM62014v1_genomic.fna/tc_result.tsv
[2024-01-25 18:03:26,646] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:03:26,647] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:03:26,647] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b864a80-0b24-4442-a50f-b90d02996ba7/dqc_reference/checkm_data
[2024-01-25 18:03:26,647] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:03:26,685] [INFO] Task started: CheckM
[2024-01-25 18:03:26,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000620145.1_ASM62014v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000620145.1_ASM62014v1_genomic.fna/checkm_input GCF_000620145.1_ASM62014v1_genomic.fna/checkm_result
[2024-01-25 18:03:57,352] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:57,353] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:57,375] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:57,375] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:57,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000620145.1_ASM62014v1_genomic.fna/markers.fasta)
[2024-01-25 18:03:57,376] [INFO] Task started: Blastn
[2024-01-25 18:03:57,376] [INFO] Running command: blastn -query GCF_000620145.1_ASM62014v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b864a80-0b24-4442-a50f-b90d02996ba7/dqc_reference/reference_markers_gtdb.fasta -out GCF_000620145.1_ASM62014v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:58,443] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:58,445] [INFO] Selected 10 target genomes.
[2024-01-25 18:03:58,446] [INFO] Target genome list was writen to GCF_000620145.1_ASM62014v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:58,454] [INFO] Task started: fastANI
[2024-01-25 18:03:58,455] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e4c299b-4d7e-4e7f-975d-309636eeef49/GCF_000620145.1_ASM62014v1_genomic.fna.gz --refList GCF_000620145.1_ASM62014v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000620145.1_ASM62014v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:04:06,908] [INFO] Task succeeded: fastANI
[2024-01-25 18:04:06,915] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:04:06,915] [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_000620145.1	s__Deefgea rivuli	100.0	1226	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Deefgea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016881405.1	s__Deefgea chitinilytica	81.1675	693	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Deefgea	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013284055.1	s__Deefgea sp013284055	80.3993	599	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Deefgea	95.0	95.22	95.22	0.87	0.87	2	-
GCF_009760905.1	s__Chitinibacter sp009760905	78.3074	359	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013403565.1	s__Chitinibacter sp013403565	78.2818	369	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013423785.1	s__Chitinibacter fontanus	78.0679	355	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429785.1	s__Chitinibacter tainanensis	77.481	296	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Chitinibacter	95.0	96.34	96.34	0.90	0.90	2	-
GCF_004194535.1	s__Iodobacter fluviatilis_A	77.3811	167	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003952345.1	s__Iodobacter sp003952345	76.8293	149	1227	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:04:06,917] [INFO] GTDB search result was written to GCF_000620145.1_ASM62014v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:04:06,917] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:04:06,919] [INFO] DFAST_QC result json was written to GCF_000620145.1_ASM62014v1_genomic.fna/dqc_result.json
[2024-01-25 18:04:06,920] [INFO] DFAST_QC completed!
[2024-01-25 18:04:06,920] [INFO] Total running time: 0h1m1s