[2024-01-24 14:11:51,220] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:51,223] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:51,223] [INFO] DQC Reference Directory: /var/lib/cwl/stgff3698a8-408a-4abf-a293-590e555c61a0/dqc_reference
[2024-01-24 14:11:52,525] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:52,531] [INFO] Task started: Prodigal
[2024-01-24 14:11:52,531] [INFO] Running command: gunzip -c /var/lib/cwl/stg988422b9-0a13-46be-a0f9-a6eecc90a103/GCF_024832785.1_ASM2483278v2_genomic.fna.gz | prodigal -d GCF_024832785.1_ASM2483278v2_genomic.fna/cds.fna -a GCF_024832785.1_ASM2483278v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:44,638] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:44,639] [INFO] Task started: HMMsearch
[2024-01-24 14:12:44,639] [INFO] Running command: hmmsearch --tblout GCF_024832785.1_ASM2483278v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff3698a8-408a-4abf-a293-590e555c61a0/dqc_reference/reference_markers.hmm GCF_024832785.1_ASM2483278v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:45,140] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:45,141] [INFO] Found 6/6 markers.
[2024-01-24 14:12:45,192] [INFO] Query marker FASTA was written to GCF_024832785.1_ASM2483278v2_genomic.fna/markers.fasta
[2024-01-24 14:12:45,193] [INFO] Task started: Blastn
[2024-01-24 14:12:45,193] [INFO] Running command: blastn -query GCF_024832785.1_ASM2483278v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgff3698a8-408a-4abf-a293-590e555c61a0/dqc_reference/reference_markers.fasta -out GCF_024832785.1_ASM2483278v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:49,288] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:49,299] [INFO] Selected 24 target genomes.
[2024-01-24 14:12:49,300] [INFO] Target genome list was writen to GCF_024832785.1_ASM2483278v2_genomic.fna/target_genomes.txt
[2024-01-24 14:12:49,402] [INFO] Task started: fastANI
[2024-01-24 14:12:49,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg988422b9-0a13-46be-a0f9-a6eecc90a103/GCF_024832785.1_ASM2483278v2_genomic.fna.gz --refList GCF_024832785.1_ASM2483278v2_genomic.fna/target_genomes.txt --output GCF_024832785.1_ASM2483278v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:13:03,572] [INFO] Task succeeded: fastANI
[2024-01-24 14:13:03,573] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff3698a8-408a-4abf-a293-590e555c61a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:13:03,573] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff3698a8-408a-4abf-a293-590e555c61a0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:13:03,580] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:13:03,580] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:13:03,580] [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
Limisphaera ngatamarikiensis	strain=NGM72.4	GCA_011044775.1	1324935	1324935	type	True	76.6676	90	1575	95	below_threshold
Vineibacter terrae	strain=CC-CFT640	GCA_008039615.1	2586908	2586908	type	True	74.8248	57	1575	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:13:03,583] [INFO] DFAST Taxonomy check result was written to GCF_024832785.1_ASM2483278v2_genomic.fna/tc_result.tsv
[2024-01-24 14:13:03,584] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:13:03,584] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:13:03,585] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff3698a8-408a-4abf-a293-590e555c61a0/dqc_reference/checkm_data
[2024-01-24 14:13:03,586] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:13:03,637] [INFO] Task started: CheckM
[2024-01-24 14:13:03,637] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024832785.1_ASM2483278v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024832785.1_ASM2483278v2_genomic.fna/checkm_input GCF_024832785.1_ASM2483278v2_genomic.fna/checkm_result
[2024-01-24 14:15:14,532] [INFO] Task succeeded: CheckM
[2024-01-24 14:15:14,533] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:15:14,566] [INFO] ===== Completeness check finished =====
[2024-01-24 14:15:14,566] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:15:14,567] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024832785.1_ASM2483278v2_genomic.fna/markers.fasta)
[2024-01-24 14:15:14,567] [INFO] Task started: Blastn
[2024-01-24 14:15:14,567] [INFO] Running command: blastn -query GCF_024832785.1_ASM2483278v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgff3698a8-408a-4abf-a293-590e555c61a0/dqc_reference/reference_markers_gtdb.fasta -out GCF_024832785.1_ASM2483278v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:15,772] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:15,776] [INFO] Selected 25 target genomes.
[2024-01-24 14:15:15,776] [INFO] Target genome list was writen to GCF_024832785.1_ASM2483278v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:15:15,827] [INFO] Task started: fastANI
[2024-01-24 14:15:15,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg988422b9-0a13-46be-a0f9-a6eecc90a103/GCF_024832785.1_ASM2483278v2_genomic.fna.gz --refList GCF_024832785.1_ASM2483278v2_genomic.fna/target_genomes_gtdb.txt --output GCF_024832785.1_ASM2483278v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:15:35,763] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:35,845] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:15:35,845] [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_011368065.1	s__DSWX01 sp011368065	78.9356	635	1575	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__CAIYYI01;g__DSWX01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011368315.1	s__DSVO01 sp011368315	76.8071	277	1575	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__CAIYYI01;g__DSVO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011044775.1	s__Limisphaera ngatamarikiensis	76.6933	89	1575	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__NGM72-4;g__Limisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716505.1	s__JADJWF01 sp016716505	76.6884	125	1575	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__JADJWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011058495.1	s__Limisphaera sp011058495	76.3572	103	1575	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__NGM72-4;g__Limisphaera	95.0	99.99	99.98	0.99	0.99	4	-
GCA_002385705.1	s__UBA3939 sp002385705	76.28	64	1575	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA3939;g__UBA3939	95.0	99.95	99.95	0.96	0.96	2	-
GCA_016871615.1	s__SXXZ01 sp016871615	76.2528	64	1575	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA9464;g__SXXZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011367605.1	s__DSYF01 sp011367605	76.2043	129	1575	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__DSYF01;g__DSYF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525685.1	s__WYBW01 sp011525685	76.1012	113	1575	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__WYBW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903872345.1	s__UBA11358 sp903872345	76.0562	103	1575	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	100.00	100.00	0.99	0.99	3	-
GCA_003695015.1	s__J093 sp003695015	76.0528	92	1575	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__J093	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773355.1	s__SXTU01 sp009773355	76.0434	121	1575	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	99.99	99.99	0.98	0.97	3	-
GCA_017880715.1	s__JADGRT01 sp017880715	76.0225	72	1575	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__JADGRT01;g__JADGRT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003138485.1	s__Palsa-1400 sp003138485	75.9574	84	1575	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__Palsa-1400;g__Palsa-1400	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930345.1	s__CAIYYI01 sp903930345	75.9418	164	1575	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__CAIYYI01;g__CAIYYI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903912925.1	s__PALSA-1440 sp903912925	75.9137	85	1575	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA8199;g__PALSA-1440	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903845125.1	s__CAIMWS01 sp903845125	75.8078	116	1575	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1319;g__CAIMWS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903944085.1	s__UBA11358 sp903944085	75.7753	90	1575	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.64	99.63	0.93	0.93	3	-
GCA_903895255.1	s__UBA11358 sp903895255	75.7069	104	1575	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.95	99.95	0.98	0.98	2	-
GCA_903863315.1	s__SXTU01 sp903863315	75.6255	87	1575	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:15:35,847] [INFO] GTDB search result was written to GCF_024832785.1_ASM2483278v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:15:35,848] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:15:35,852] [INFO] DFAST_QC result json was written to GCF_024832785.1_ASM2483278v2_genomic.fna/dqc_result.json
[2024-01-24 14:15:35,852] [INFO] DFAST_QC completed!
[2024-01-24 14:15:35,852] [INFO] Total running time: 0h3m45s