[2024-01-24 14:22:33,483] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:33,491] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:33,492] [INFO] DQC Reference Directory: /var/lib/cwl/stg527f5932-0ab4-41a3-9e2c-8edfeb85484a/dqc_reference
[2024-01-24 14:22:34,789] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:34,790] [INFO] Task started: Prodigal
[2024-01-24 14:22:34,790] [INFO] Running command: gunzip -c /var/lib/cwl/stg281af406-d26d-4246-8381-abd1735a8f33/GCF_014202995.1_ASM1420299v1_genomic.fna.gz | prodigal -d GCF_014202995.1_ASM1420299v1_genomic.fna/cds.fna -a GCF_014202995.1_ASM1420299v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:00,175] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:00,175] [INFO] Task started: HMMsearch
[2024-01-24 14:23:00,175] [INFO] Running command: hmmsearch --tblout GCF_014202995.1_ASM1420299v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg527f5932-0ab4-41a3-9e2c-8edfeb85484a/dqc_reference/reference_markers.hmm GCF_014202995.1_ASM1420299v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:00,534] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:00,536] [INFO] Found 6/6 markers.
[2024-01-24 14:23:00,592] [INFO] Query marker FASTA was written to GCF_014202995.1_ASM1420299v1_genomic.fna/markers.fasta
[2024-01-24 14:23:00,592] [INFO] Task started: Blastn
[2024-01-24 14:23:00,593] [INFO] Running command: blastn -query GCF_014202995.1_ASM1420299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg527f5932-0ab4-41a3-9e2c-8edfeb85484a/dqc_reference/reference_markers.fasta -out GCF_014202995.1_ASM1420299v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:01,378] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:01,413] [INFO] Selected 14 target genomes.
[2024-01-24 14:23:01,414] [INFO] Target genome list was writen to GCF_014202995.1_ASM1420299v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:01,426] [INFO] Task started: fastANI
[2024-01-24 14:23:01,426] [INFO] Running command: fastANI --query /var/lib/cwl/stg281af406-d26d-4246-8381-abd1735a8f33/GCF_014202995.1_ASM1420299v1_genomic.fna.gz --refList GCF_014202995.1_ASM1420299v1_genomic.fna/target_genomes.txt --output GCF_014202995.1_ASM1420299v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:28,251] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:28,252] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg527f5932-0ab4-41a3-9e2c-8edfeb85484a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:28,252] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg527f5932-0ab4-41a3-9e2c-8edfeb85484a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:28,263] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:23:28,263] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:28,264] [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
Longimicrobium terrae	strain=DSM 29007	GCA_014202995.1	1639882	1639882	type	True	100.0	2232	2233	95	conclusive
Longimicrobium terrae	strain=CECT 8660	GCA_014198875.1	1639882	1639882	type	True	99.9991	2232	2233	95	conclusive
Longimicrobium terrae	strain=CB-286315	GCA_013000925.1	1639882	1639882	type	True	99.9964	2230	2233	95	conclusive
Gemmatirosa kalamazoonensis	strain=KBS708	GCA_000522985.1	861299	861299	type	True	75.5205	387	2233	95	below_threshold
Gemmatimonas groenlandica	strain=TET16	GCA_013004105.1	2732249	2732249	type	True	75.358	102	2233	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	75.3266	435	2233	95	below_threshold
Corallococcus llansteffanensis	strain=CA051B	GCA_003612055.1	2316731	2316731	type	True	75.317	351	2233	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	75.146	293	2233	95	below_threshold
Crenobacter intestini	strain=GY 70310	GCA_004919095.1	2563443	2563443	type	True	74.9161	106	2233	95	below_threshold
Kutzneria kofuensis	strain=DSM 43851	GCA_014203355.1	103725	103725	type	True	74.8767	297	2233	95	below_threshold
Deferrisoma camini	strain=S3R1	GCA_000526155.1	1035120	1035120	type	True	74.8628	94	2233	95	below_threshold
Pseudoscardovia radai	strain=DSM 24742	GCA_002259605.1	987066	987066	type	True	74.6927	53	2233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:28,266] [INFO] DFAST Taxonomy check result was written to GCF_014202995.1_ASM1420299v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:28,267] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:28,267] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:28,267] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg527f5932-0ab4-41a3-9e2c-8edfeb85484a/dqc_reference/checkm_data
[2024-01-24 14:23:28,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:28,337] [INFO] Task started: CheckM
[2024-01-24 14:23:28,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014202995.1_ASM1420299v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014202995.1_ASM1420299v1_genomic.fna/checkm_input GCF_014202995.1_ASM1420299v1_genomic.fna/checkm_result
[2024-01-24 14:24:49,948] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:49,949] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:49,974] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:49,975] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:49,975] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014202995.1_ASM1420299v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:49,976] [INFO] Task started: Blastn
[2024-01-24 14:24:49,976] [INFO] Running command: blastn -query GCF_014202995.1_ASM1420299v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg527f5932-0ab4-41a3-9e2c-8edfeb85484a/dqc_reference/reference_markers_gtdb.fasta -out GCF_014202995.1_ASM1420299v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:51,071] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:51,075] [INFO] Selected 18 target genomes.
[2024-01-24 14:24:51,076] [INFO] Target genome list was writen to GCF_014202995.1_ASM1420299v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:51,094] [INFO] Task started: fastANI
[2024-01-24 14:24:51,094] [INFO] Running command: fastANI --query /var/lib/cwl/stg281af406-d26d-4246-8381-abd1735a8f33/GCF_014202995.1_ASM1420299v1_genomic.fna.gz --refList GCF_014202995.1_ASM1420299v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014202995.1_ASM1420299v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:25:09,571] [INFO] Task succeeded: fastANI
[2024-01-24 14:25:09,585] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:25:09,586] [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_014202995.1	s__Longimicrobium terrae	100.0	2232	2233	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__Longimicrobiaceae;g__Longimicrobium	95.0	100.00	100.00	1.00	1.00	3	conclusive
GCA_902805735.1	s__Longimicrobium sp902805735	78.9208	767	2233	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__Longimicrobiaceae;g__Longimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019240375.1	s__JAFAYN01 sp019240375	77.7069	348	2233	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__Longimicrobiaceae;g__JAFAYN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013820915.1	s__JACDHR01 sp013820915	76.5923	215	2233	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__Longimicrobiaceae;g__JACDHR01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007118565.1	s__SKRI01 sp007118565	76.2861	155	2233	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__Longimicrobiaceae;g__SKRI01	95.0	99.36	99.36	0.87	0.87	2	-
GCA_016741895.1	s__Gemmatimonas sp016741895	75.8903	130	2233	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__Gemmatimonadaceae;g__Gemmatimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015492755.1	s__S146-37 sp015492755	75.835	107	2233	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__S146-37	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003242735.1	s__RSA9 sp003242735	75.6869	211	2233	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__RSA9;g__RSA9	95.0	99.82	99.82	0.92	0.92	2	-
GCA_016873995.1	s__UBA2982 sp016873995	75.6516	108	2233	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2982	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011774835.1	s__KS3-K002 sp011774835	75.5944	92	2233	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__KS3-K002;f__KS3-K002;g__KS3-K002	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794805.1	s__JADJOM01 sp016794805	75.5887	171	2233	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JADJOM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713785.1	s__JADJOM01 sp016713785	75.58	231	2233	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JADJOM01	95.0	99.05	98.46	0.95	0.91	10	-
GCA_013002885.1	s__UBA2589 sp013002885	75.511	62	2233	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__UBA2589	95.0	99.00	99.00	0.85	0.85	2	-
GCA_017889745.1	s__JAGGAG01 sp017889745	75.4093	107	2233	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Gemmatimonadales;f__GWC2-71-9;g__JAGGAG01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016209885.1	s__JACQVF01 sp016209885	75.2876	110	2233	d__Bacteria;p__Gemmatimonadota;c__Gemmatimonadetes;o__Longimicrobiales;f__UBA6960;g__JACQVF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623495.1	s__JAAZVP01 sp018623495	75.1473	82	2233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Halothiobacillales;f__JAAZVP01;g__JAAZVP01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:25:09,589] [INFO] GTDB search result was written to GCF_014202995.1_ASM1420299v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:25:09,590] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:25:09,594] [INFO] DFAST_QC result json was written to GCF_014202995.1_ASM1420299v1_genomic.fna/dqc_result.json
[2024-01-24 14:25:09,594] [INFO] DFAST_QC completed!
[2024-01-24 14:25:09,594] [INFO] Total running time: 0h2m36s