[2023-06-27 18:56:01,832] [INFO] DFAST_QC pipeline started.
[2023-06-27 18:56:01,834] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 18:56:01,834] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7cbb72c-ad06-4cf5-a678-d859857082bb/dqc_reference
[2023-06-27 18:56:03,901] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 18:56:03,902] [INFO] Task started: Prodigal
[2023-06-27 18:56:03,902] [INFO] Running command: gunzip -c /var/lib/cwl/stg5fe5c57b-24ad-4aeb-8ff1-7ecf3894d4ea/GCA_026989475.1_ASM2698947v1_genomic.fna.gz | prodigal -d GCA_026989475.1_ASM2698947v1_genomic.fna/cds.fna -a GCA_026989475.1_ASM2698947v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 18:56:10,361] [INFO] Task succeeded: Prodigal
[2023-06-27 18:56:10,362] [INFO] Task started: HMMsearch
[2023-06-27 18:56:10,362] [INFO] Running command: hmmsearch --tblout GCA_026989475.1_ASM2698947v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7cbb72c-ad06-4cf5-a678-d859857082bb/dqc_reference/reference_markers.hmm GCA_026989475.1_ASM2698947v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 18:56:10,554] [INFO] Task succeeded: HMMsearch
[2023-06-27 18:56:10,556] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5fe5c57b-24ad-4aeb-8ff1-7ecf3894d4ea/GCA_026989475.1_ASM2698947v1_genomic.fna.gz]
[2023-06-27 18:56:10,578] [INFO] Query marker FASTA was written to GCA_026989475.1_ASM2698947v1_genomic.fna/markers.fasta
[2023-06-27 18:56:10,579] [INFO] Task started: Blastn
[2023-06-27 18:56:10,579] [INFO] Running command: blastn -query GCA_026989475.1_ASM2698947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7cbb72c-ad06-4cf5-a678-d859857082bb/dqc_reference/reference_markers.fasta -out GCA_026989475.1_ASM2698947v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:56:11,184] [INFO] Task succeeded: Blastn
[2023-06-27 18:56:11,188] [INFO] Selected 10 target genomes.
[2023-06-27 18:56:11,188] [INFO] Target genome list was writen to GCA_026989475.1_ASM2698947v1_genomic.fna/target_genomes.txt
[2023-06-27 18:56:11,190] [INFO] Task started: fastANI
[2023-06-27 18:56:11,190] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fe5c57b-24ad-4aeb-8ff1-7ecf3894d4ea/GCA_026989475.1_ASM2698947v1_genomic.fna.gz --refList GCA_026989475.1_ASM2698947v1_genomic.fna/target_genomes.txt --output GCA_026989475.1_ASM2698947v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 18:56:15,022] [INFO] Task succeeded: fastANI
[2023-06-27 18:56:15,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7cbb72c-ad06-4cf5-a678-d859857082bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 18:56:15,023] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7cbb72c-ad06-4cf5-a678-d859857082bb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 18:56:15,033] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 18:56:15,033] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 18:56:15,033] [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
Oceanithermus desulfurans	strain=NBRC 100063	GCA_007991015.1	227924	227924	type	True	78.5838	152	325	95	below_threshold
Oceanithermus desulfurans	strain=DSM 15757	GCA_014201675.1	227924	227924	type	True	78.4876	158	325	95	below_threshold
Oceanithermus profundus	strain=DSM 14977	GCA_000183745.1	187137	187137	type	True	78.2617	169	325	95	below_threshold
Thermus thermophilus	strain=HB8	GCA_000091545.1	274	274	type	True	77.5333	118	325	95	below_threshold
Thermus thermophilus	strain=JCM10941	GCA_019973715.1	274	274	type	True	77.4826	119	325	95	below_threshold
Thermus parvatiensis	strain=RL	GCA_000252835.2	456163	456163	type	True	77.2665	101	325	95	below_threshold
Marinithermus hydrothermalis	strain=DSM 14884	GCA_000195335.1	186192	186192	type	True	77.2552	92	325	95	below_threshold
Calidithermus chliarophilus	strain=DSM 9957	GCA_000430045.1	52023	52023	type	True	77.0888	115	325	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 18:56:15,035] [INFO] DFAST Taxonomy check result was written to GCA_026989475.1_ASM2698947v1_genomic.fna/tc_result.tsv
[2023-06-27 18:56:15,036] [INFO] ===== Taxonomy check completed =====
[2023-06-27 18:56:15,036] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 18:56:15,036] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7cbb72c-ad06-4cf5-a678-d859857082bb/dqc_reference/checkm_data
[2023-06-27 18:56:15,037] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 18:56:15,054] [INFO] Task started: CheckM
[2023-06-27 18:56:15,054] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026989475.1_ASM2698947v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026989475.1_ASM2698947v1_genomic.fna/checkm_input GCA_026989475.1_ASM2698947v1_genomic.fna/checkm_result
[2023-06-27 18:56:38,925] [INFO] Task succeeded: CheckM
[2023-06-27 18:56:38,927] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.73%
Contamintation: 2.60%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-27 18:56:38,955] [INFO] ===== Completeness check finished =====
[2023-06-27 18:56:38,955] [INFO] ===== Start GTDB Search =====
[2023-06-27 18:56:38,956] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026989475.1_ASM2698947v1_genomic.fna/markers.fasta)
[2023-06-27 18:56:38,956] [INFO] Task started: Blastn
[2023-06-27 18:56:38,956] [INFO] Running command: blastn -query GCA_026989475.1_ASM2698947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7cbb72c-ad06-4cf5-a678-d859857082bb/dqc_reference/reference_markers_gtdb.fasta -out GCA_026989475.1_ASM2698947v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:56:39,854] [INFO] Task succeeded: Blastn
[2023-06-27 18:56:39,858] [INFO] Selected 8 target genomes.
[2023-06-27 18:56:39,858] [INFO] Target genome list was writen to GCA_026989475.1_ASM2698947v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 18:56:39,864] [INFO] Task started: fastANI
[2023-06-27 18:56:39,864] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fe5c57b-24ad-4aeb-8ff1-7ecf3894d4ea/GCA_026989475.1_ASM2698947v1_genomic.fna.gz --refList GCA_026989475.1_ASM2698947v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026989475.1_ASM2698947v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 18:56:43,022] [INFO] Task succeeded: fastANI
[2023-06-27 18:56:43,030] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 18:56:43,031] [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
GCA_015490435.1	s__WFXV01 sp015490435	90.3234	260	325	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__WFXV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015488545.1	s__WFXV01 sp015488545	81.0385	220	325	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__WFXV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015519965.1	s__WFXV01 sp015519965	78.6814	130	325	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__WFXV01	95.0	99.28	99.28	0.73	0.73	2	-
GCF_014201675.1	s__Oceanithermus desulfurans	78.4876	158	325	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	97.68	96.67	0.93	0.89	5	-
GCA_015494055.1	s__Oceanithermus sp015494055	78.336	134	325	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	99.03	99.03	0.84	0.84	2	-
GCF_000183745.1	s__Oceanithermus profundus	78.2821	168	325	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011330655.1	s__Oceanithermus profundus_A	78.0961	129	325	d__Bacteria;p__Deinococcota;c__Deinococci;o__Deinococcales;f__Marinithermaceae;g__Oceanithermus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 18:56:43,035] [INFO] GTDB search result was written to GCA_026989475.1_ASM2698947v1_genomic.fna/result_gtdb.tsv
[2023-06-27 18:56:43,036] [INFO] ===== GTDB Search completed =====
[2023-06-27 18:56:43,039] [INFO] DFAST_QC result json was written to GCA_026989475.1_ASM2698947v1_genomic.fna/dqc_result.json
[2023-06-27 18:56:43,040] [INFO] DFAST_QC completed!
[2023-06-27 18:56:43,040] [INFO] Total running time: 0h0m41s