[2024-01-24 15:26:55,130] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:55,133] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:55,133] [INFO] DQC Reference Directory: /var/lib/cwl/stge4d00664-08d0-434f-81ac-7f40729ff0d9/dqc_reference
[2024-01-24 15:26:56,409] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:56,410] [INFO] Task started: Prodigal
[2024-01-24 15:26:56,411] [INFO] Running command: gunzip -c /var/lib/cwl/stg45c09092-e69f-473c-8420-497af6c4a1a6/GCF_003952345.1_ASM395234v1_genomic.fna.gz | prodigal -d GCF_003952345.1_ASM395234v1_genomic.fna/cds.fna -a GCF_003952345.1_ASM395234v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:06,949] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:06,949] [INFO] Task started: HMMsearch
[2024-01-24 15:27:06,949] [INFO] Running command: hmmsearch --tblout GCF_003952345.1_ASM395234v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge4d00664-08d0-434f-81ac-7f40729ff0d9/dqc_reference/reference_markers.hmm GCF_003952345.1_ASM395234v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:07,225] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:07,227] [INFO] Found 6/6 markers.
[2024-01-24 15:27:07,262] [INFO] Query marker FASTA was written to GCF_003952345.1_ASM395234v1_genomic.fna/markers.fasta
[2024-01-24 15:27:07,263] [INFO] Task started: Blastn
[2024-01-24 15:27:07,263] [INFO] Running command: blastn -query GCF_003952345.1_ASM395234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4d00664-08d0-434f-81ac-7f40729ff0d9/dqc_reference/reference_markers.fasta -out GCF_003952345.1_ASM395234v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:07,970] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:07,973] [INFO] Selected 15 target genomes.
[2024-01-24 15:27:07,974] [INFO] Target genome list was writen to GCF_003952345.1_ASM395234v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:07,979] [INFO] Task started: fastANI
[2024-01-24 15:27:07,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg45c09092-e69f-473c-8420-497af6c4a1a6/GCF_003952345.1_ASM395234v1_genomic.fna.gz --refList GCF_003952345.1_ASM395234v1_genomic.fna/target_genomes.txt --output GCF_003952345.1_ASM395234v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:20,052] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:20,053] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge4d00664-08d0-434f-81ac-7f40729ff0d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:20,053] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge4d00664-08d0-434f-81ac-7f40729ff0d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:20,065] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:20,066] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:20,066] [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
Iodobacter ciconiae	strain=H11R3	GCA_003952345.1	2496266	2496266	type	True	100.0	1291	1292	95	conclusive
Iodobacter fluviatilis	strain=NCTC11159	GCA_900451195.1	537	537	type	True	84.7253	992	1292	95	below_threshold
Iodobacter fluviatilis	strain=DSM 3764	GCA_004346505.1	537	537	type	True	84.5094	965	1292	95	below_threshold
Chitinibacter fontanus	strain=STM-7	GCA_013423785.1	1737446	1737446	type	True	78.1159	120	1292	95	below_threshold
Deefgea salmonis	strain=H3-26	GCA_020531905.1	2875502	2875502	type	True	77.4211	126	1292	95	below_threshold
Silvimonas terrae	strain=DSM 18233	GCA_014202765.1	300266	300266	type	True	76.8765	106	1292	95	below_threshold
Deefgea rivuli	strain=DSM 18356	GCA_000620145.1	400948	400948	type	True	76.8304	153	1292	95	below_threshold
Chitinibacter tainanensis	strain=DSM 15459	GCA_000429785.1	230667	230667	type	True	76.6211	143	1292	95	below_threshold
Chitinilyticum piscinae	strain=4Y14	GCA_015223195.1	2866724	2866724	type	True	76.5164	73	1292	95	below_threshold
Chitiniphilus eburneus	strain=HX-2-15	GCA_005048205.1	2571148	2571148	type	True	76.4503	71	1292	95	below_threshold
Andreprevotia lacus	strain=DSM 23236	GCA_900176275.1	1121000	1121000	type	True	76.4219	85	1292	95	below_threshold
Chitinilyticum litopenaei	strain=DSM 21440	GCA_000428145.1	1121276	1121276	type	True	76.2512	77	1292	95	below_threshold
Rivicola pingtungensis	strain=DSM 29661	GCA_003201855.1	1054498	1054498	type	True	75.9883	62	1292	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:20,068] [INFO] DFAST Taxonomy check result was written to GCF_003952345.1_ASM395234v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:20,068] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:20,068] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:20,069] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge4d00664-08d0-434f-81ac-7f40729ff0d9/dqc_reference/checkm_data
[2024-01-24 15:27:20,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:20,114] [INFO] Task started: CheckM
[2024-01-24 15:27:20,114] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003952345.1_ASM395234v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003952345.1_ASM395234v1_genomic.fna/checkm_input GCF_003952345.1_ASM395234v1_genomic.fna/checkm_result
[2024-01-24 15:27:54,196] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:54,197] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:54,216] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:54,216] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:54,217] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003952345.1_ASM395234v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:54,217] [INFO] Task started: Blastn
[2024-01-24 15:27:54,217] [INFO] Running command: blastn -query GCF_003952345.1_ASM395234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge4d00664-08d0-434f-81ac-7f40729ff0d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_003952345.1_ASM395234v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:55,283] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:55,286] [INFO] Selected 5 target genomes.
[2024-01-24 15:27:55,286] [INFO] Target genome list was writen to GCF_003952345.1_ASM395234v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:55,290] [INFO] Task started: fastANI
[2024-01-24 15:27:55,291] [INFO] Running command: fastANI --query /var/lib/cwl/stg45c09092-e69f-473c-8420-497af6c4a1a6/GCF_003952345.1_ASM395234v1_genomic.fna.gz --refList GCF_003952345.1_ASM395234v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003952345.1_ASM395234v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:02,258] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:02,264] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:02,264] [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_003952345.1	s__Iodobacter sp003952345	100.0	1291	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002735645.1	s__Iodobacter sp002735645	84.9215	962	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011601265.1	s__Iodobacter sp011601265	84.8534	983	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900451195.1	s__Iodobacter fluviatilis	84.6811	995	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000969645.2	s__Iodobacter sp000969645	84.016	952	1292	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Chitinibacteraceae;g__Iodobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:02,266] [INFO] GTDB search result was written to GCF_003952345.1_ASM395234v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:02,267] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:02,270] [INFO] DFAST_QC result json was written to GCF_003952345.1_ASM395234v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:02,270] [INFO] DFAST_QC completed!
[2024-01-24 15:28:02,270] [INFO] Total running time: 0h1m7s