[2024-01-25 18:16:35,484] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:16:35,486] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:16:35,486] [INFO] DQC Reference Directory: /var/lib/cwl/stg94a9738d-f12d-4643-a4b0-328d8e918f2d/dqc_reference
[2024-01-25 18:16:36,644] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:16:36,645] [INFO] Task started: Prodigal
[2024-01-25 18:16:36,645] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ae22ffa-e33c-4229-8266-8c787c61ef4c/GCF_000471025.2_ASM47102v2_genomic.fna.gz | prodigal -d GCF_000471025.2_ASM47102v2_genomic.fna/cds.fna -a GCF_000471025.2_ASM47102v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:16:38,440] [INFO] Task succeeded: Prodigal
[2024-01-25 18:16:38,440] [INFO] Task started: HMMsearch
[2024-01-25 18:16:38,440] [INFO] Running command: hmmsearch --tblout GCF_000471025.2_ASM47102v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94a9738d-f12d-4643-a4b0-328d8e918f2d/dqc_reference/reference_markers.hmm GCF_000471025.2_ASM47102v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:16:38,626] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:16:38,627] [INFO] Found 6/6 markers.
[2024-01-25 18:16:38,641] [INFO] Query marker FASTA was written to GCF_000471025.2_ASM47102v2_genomic.fna/markers.fasta
[2024-01-25 18:16:38,641] [INFO] Task started: Blastn
[2024-01-25 18:16:38,641] [INFO] Running command: blastn -query GCF_000471025.2_ASM47102v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg94a9738d-f12d-4643-a4b0-328d8e918f2d/dqc_reference/reference_markers.fasta -out GCF_000471025.2_ASM47102v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:39,165] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:39,167] [INFO] Selected 13 target genomes.
[2024-01-25 18:16:39,168] [INFO] Target genome list was writen to GCF_000471025.2_ASM47102v2_genomic.fna/target_genomes.txt
[2024-01-25 18:16:39,187] [INFO] Task started: fastANI
[2024-01-25 18:16:39,187] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ae22ffa-e33c-4229-8266-8c787c61ef4c/GCF_000471025.2_ASM47102v2_genomic.fna.gz --refList GCF_000471025.2_ASM47102v2_genomic.fna/target_genomes.txt --output GCF_000471025.2_ASM47102v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:16:42,439] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:42,439] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94a9738d-f12d-4643-a4b0-328d8e918f2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:16:42,439] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94a9738d-f12d-4643-a4b0-328d8e918f2d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:16:42,448] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:16:42,448] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:16:42,448] [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
Chlamydia gallinacea	strain=08-1274/3	GCA_000471025.2	1457153	1457153	type	True	100.0	355	355	95	conclusive
Chlamydia avium	strain=10DC88	GCA_000583875.1	1457141	1457141	type	True	81.9701	311	355	95	below_threshold
Chlamydia caviae		GCA_000007605.1	83557	83557	type	True	78.4791	151	355	95	below_threshold
Chlamydia buteonis		GCA_900634605.1	2494525	2494525	type	True	78.2569	152	355	95	below_threshold
Chlamydia poikilotherma	strain=S15-834K	GCA_900239975.1	1967783	1967783	type	True	78.256	166	355	95	below_threshold
Chlamydia abortus	strain=GIMC 2006:CabB577	GCA_002895085.1	83555	83555	type	True	78.1017	138	355	95	below_threshold
Chlamydia psittaci	strain=6BC	GCA_000204255.1	83554	83554	type	True	78.0462	156	355	95	below_threshold
Chlamydia psittaci	strain=6BC	GCA_000191925.1	83554	83554	type	True	78.0303	157	355	95	below_threshold
Chlamydia pecorum	strain=E58	GCA_000204135.1	85991	85991	type	True	77.7067	61	355	95	below_threshold
Chlamydia serpentis	strain=H15-1957-10C	GCA_900239945.1	1967782	1967782	type	True	77.4479	73	355	95	below_threshold
Chlamydia ibidis	strain=10-1398/6	GCA_000454725.1	1405396	1405396	type	True	77.427	87	355	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:16:42,450] [INFO] DFAST Taxonomy check result was written to GCF_000471025.2_ASM47102v2_genomic.fna/tc_result.tsv
[2024-01-25 18:16:42,450] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:16:42,451] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:16:42,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94a9738d-f12d-4643-a4b0-328d8e918f2d/dqc_reference/checkm_data
[2024-01-25 18:16:42,452] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:16:42,465] [INFO] Task started: CheckM
[2024-01-25 18:16:42,465] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000471025.2_ASM47102v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000471025.2_ASM47102v2_genomic.fna/checkm_input GCF_000471025.2_ASM47102v2_genomic.fna/checkm_result
[2024-01-25 18:16:54,760] [INFO] Task succeeded: CheckM
[2024-01-25 18:16:54,762] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:16:54,779] [INFO] ===== Completeness check finished =====
[2024-01-25 18:16:54,779] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:16:54,780] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000471025.2_ASM47102v2_genomic.fna/markers.fasta)
[2024-01-25 18:16:54,780] [INFO] Task started: Blastn
[2024-01-25 18:16:54,780] [INFO] Running command: blastn -query GCF_000471025.2_ASM47102v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg94a9738d-f12d-4643-a4b0-328d8e918f2d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000471025.2_ASM47102v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:16:55,521] [INFO] Task succeeded: Blastn
[2024-01-25 18:16:55,525] [INFO] Selected 17 target genomes.
[2024-01-25 18:16:55,525] [INFO] Target genome list was writen to GCF_000471025.2_ASM47102v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:16:55,549] [INFO] Task started: fastANI
[2024-01-25 18:16:55,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ae22ffa-e33c-4229-8266-8c787c61ef4c/GCF_000471025.2_ASM47102v2_genomic.fna.gz --refList GCF_000471025.2_ASM47102v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000471025.2_ASM47102v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:16:59,746] [INFO] Task succeeded: fastANI
[2024-01-25 18:16:59,755] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:16:59,755] [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_000471025.2	s__Chlamydophila gallinacea	100.0	355	355	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila	95.0	99.52	99.52	0.99	0.99	2	conclusive
GCF_000583875.1	s__Chlamydophila avium	81.9701	311	355	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila	95.0	99.57	99.56	1.00	0.99	4	-
GCF_000007605.1	s__Chlamydophila caviae	78.4791	151	355	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900634605.1	s__Chlamydophila buteonis	78.2569	152	355	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila	95.0	99.99	99.99	1.00	1.00	3	-
GCF_900239975.1	s__Chlamydophila sp900239975	78.256	166	355	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002895085.1	s__Chlamydophila abortus	78.1017	138	355	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila	95.0	99.82	97.53	0.99	0.97	57	-
GCF_000204255.1	s__Chlamydophila psittaci	78.0462	156	355	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila	95.0	99.65	97.64	1.00	0.97	66	-
GCF_000009945.1	s__Chlamydophila felis	77.9562	137	355	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000204135.1	s__Chlamydophila pecorum	77.7067	61	355	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila	95.0	99.31	98.99	0.99	0.99	12	-
GCF_001653975.1	s__Chlamydophila sp001653975	77.5804	72	355	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000454725.1	s__Chlamydophila ibidis	77.427	87	355	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002817655.1	s__Chlamydophila corallus	77.0894	64	355	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000007205.1	s__Chlamydophila pneumoniae	76.9506	66	355	d__Bacteria;p__Chlamydiota;c__Chlamydiia;o__Chlamydiales;f__Chlamydiaceae;g__Chlamydophila	95.0	99.80	99.07	1.00	0.98	13	-
--------------------------------------------------------------------------------
[2024-01-25 18:16:59,756] [INFO] GTDB search result was written to GCF_000471025.2_ASM47102v2_genomic.fna/result_gtdb.tsv
[2024-01-25 18:16:59,757] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:16:59,759] [INFO] DFAST_QC result json was written to GCF_000471025.2_ASM47102v2_genomic.fna/dqc_result.json
[2024-01-25 18:16:59,759] [INFO] DFAST_QC completed!
[2024-01-25 18:16:59,759] [INFO] Total running time: 0h0m24s