[2023-06-18 17:35:20,907] [INFO] DFAST_QC pipeline started.
[2023-06-18 17:35:20,911] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 17:35:20,911] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2238ffb-bf10-4062-ae53-d5a5f208bbcc/dqc_reference
[2023-06-18 17:35:24,785] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 17:35:24,786] [INFO] Task started: Prodigal
[2023-06-18 17:35:24,787] [INFO] Running command: gunzip -c /var/lib/cwl/stg8d399f2f-549e-4d0d-bc3d-e0e35929fb0a/GCA_018969165.1_ASM1896916v1_genomic.fna.gz | prodigal -d GCA_018969165.1_ASM1896916v1_genomic.fna/cds.fna -a GCA_018969165.1_ASM1896916v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 17:35:54,983] [INFO] Task succeeded: Prodigal
[2023-06-18 17:35:54,983] [INFO] Task started: HMMsearch
[2023-06-18 17:35:54,983] [INFO] Running command: hmmsearch --tblout GCA_018969165.1_ASM1896916v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2238ffb-bf10-4062-ae53-d5a5f208bbcc/dqc_reference/reference_markers.hmm GCA_018969165.1_ASM1896916v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 17:35:55,314] [INFO] Task succeeded: HMMsearch
[2023-06-18 17:35:55,315] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8d399f2f-549e-4d0d-bc3d-e0e35929fb0a/GCA_018969165.1_ASM1896916v1_genomic.fna.gz]
[2023-06-18 17:35:55,364] [INFO] Query marker FASTA was written to GCA_018969165.1_ASM1896916v1_genomic.fna/markers.fasta
[2023-06-18 17:35:55,365] [INFO] Task started: Blastn
[2023-06-18 17:35:55,365] [INFO] Running command: blastn -query GCA_018969165.1_ASM1896916v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2238ffb-bf10-4062-ae53-d5a5f208bbcc/dqc_reference/reference_markers.fasta -out GCA_018969165.1_ASM1896916v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:35:56,051] [INFO] Task succeeded: Blastn
[2023-06-18 17:35:56,055] [INFO] Selected 23 target genomes.
[2023-06-18 17:35:56,056] [INFO] Target genome list was writen to GCA_018969165.1_ASM1896916v1_genomic.fna/target_genomes.txt
[2023-06-18 17:35:56,060] [INFO] Task started: fastANI
[2023-06-18 17:35:56,060] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d399f2f-549e-4d0d-bc3d-e0e35929fb0a/GCA_018969165.1_ASM1896916v1_genomic.fna.gz --refList GCA_018969165.1_ASM1896916v1_genomic.fna/target_genomes.txt --output GCA_018969165.1_ASM1896916v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 17:36:14,069] [INFO] Task succeeded: fastANI
[2023-06-18 17:36:14,071] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2238ffb-bf10-4062-ae53-d5a5f208bbcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 17:36:14,072] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2238ffb-bf10-4062-ae53-d5a5f208bbcc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 17:36:14,084] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 17:36:14,085] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 17:36:14,085] [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
Catellatospora sichuanensis	strain=H14505	GCA_007483665.1	1969805	1969805	type	True	74.6598	80	1137	95	below_threshold
Catellatospora citrea	strain=NBRC 14495	GCA_016862615.1	53366	53366	type	True	74.6442	77	1137	95	below_threshold
Phytohabitans rumicis	strain=NBRC 108638	GCA_011764445.1	1076125	1076125	type	True	74.6178	95	1137	95	below_threshold
Catellatospora paridis	strain=NEAU-CL2	GCA_009720365.1	1617086	1617086	type	True	74.6011	64	1137	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 17:36:14,088] [INFO] DFAST Taxonomy check result was written to GCA_018969165.1_ASM1896916v1_genomic.fna/tc_result.tsv
[2023-06-18 17:36:14,089] [INFO] ===== Taxonomy check completed =====
[2023-06-18 17:36:14,089] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 17:36:14,090] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2238ffb-bf10-4062-ae53-d5a5f208bbcc/dqc_reference/checkm_data
[2023-06-18 17:36:14,091] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 17:36:14,143] [INFO] Task started: CheckM
[2023-06-18 17:36:14,144] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018969165.1_ASM1896916v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018969165.1_ASM1896916v1_genomic.fna/checkm_input GCA_018969165.1_ASM1896916v1_genomic.fna/checkm_result
[2023-06-18 17:37:32,125] [INFO] Task succeeded: CheckM
[2023-06-18 17:37:32,127] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 74.82%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 17:37:32,163] [INFO] ===== Completeness check finished =====
[2023-06-18 17:37:32,164] [INFO] ===== Start GTDB Search =====
[2023-06-18 17:37:32,164] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018969165.1_ASM1896916v1_genomic.fna/markers.fasta)
[2023-06-18 17:37:32,164] [INFO] Task started: Blastn
[2023-06-18 17:37:32,165] [INFO] Running command: blastn -query GCA_018969165.1_ASM1896916v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2238ffb-bf10-4062-ae53-d5a5f208bbcc/dqc_reference/reference_markers_gtdb.fasta -out GCA_018969165.1_ASM1896916v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:37:33,133] [INFO] Task succeeded: Blastn
[2023-06-18 17:37:33,141] [INFO] Selected 25 target genomes.
[2023-06-18 17:37:33,141] [INFO] Target genome list was writen to GCA_018969165.1_ASM1896916v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 17:37:33,175] [INFO] Task started: fastANI
[2023-06-18 17:37:33,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg8d399f2f-549e-4d0d-bc3d-e0e35929fb0a/GCA_018969165.1_ASM1896916v1_genomic.fna.gz --refList GCA_018969165.1_ASM1896916v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018969165.1_ASM1896916v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 17:37:51,542] [INFO] Task succeeded: fastANI
[2023-06-18 17:37:51,558] [INFO] Found 20 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-18 17:37:51,559] [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_002385705.1	s__UBA3939 sp002385705	76.3358	74	1137	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA3939;g__UBA3939	95.0	99.95	99.95	0.96	0.96	2	-
GCA_009695285.1	s__SIBH01 sp009695285	76.3295	60	1137	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SIBH01;g__SIBH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011327785.1	s__DSVZ01 sp011327785	76.2285	120	1137	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__DSVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018006935.1	s__JAGMXM01 sp018006935	76.1827	82	1137	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1319;g__JAGMXM01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015075445.1	s__DSVZ01 sp015075445	76.023	122	1137	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__J093;g__DSVZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011367605.1	s__DSYF01 sp011367605	75.9946	119	1137	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__DSYF01;g__DSYF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003161635.1	s__UBA7542 sp003161635	75.9856	74	1137	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA7542	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003219345.1	s__AV2 sp003219345	75.8703	106	1137	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__AV2;g__AV2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016219875.1	s__JACRJZ01 sp016219875	75.8542	146	1137	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__JACRJZ01;g__JACRJZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014193395.1	s__BJHT01 sp014193395	75.777	128	1137	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__BJHT01;g__BJHT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903930565.1	s__CAIXFN01 sp903930565	75.7257	87	1137	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__Pedosphaeraceae;g__CAIXFN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016195385.1	s__JACPZS01 sp016195385	75.7239	88	1137	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__JACPZS01;g__JACPZS01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016199985.1	s__UBA11320 sp016199985	75.672	62	1137	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11320;g__UBA11320	95.0	99.90	99.90	0.99	0.99	2	-
GCA_903884535.1	s__UBA11358 sp903884535	75.6493	60	1137	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.90	99.82	0.93	0.89	5	-
GCA_903870815.1	s__UBA11358 sp903870815	75.645	59	1137	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.83	99.83	0.93	0.93	2	-
GCA_004297495.1	s__SCTL01 sp004297495	75.5114	53	1137	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__SCTL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009695195.1	s__SCTL01 sp009695195	75.4841	71	1137	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__SCTL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016190065.1	s__VHCZ01 sp016190065	75.4479	80	1137	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SIBE01;g__VHCZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903944085.1	s__UBA11358 sp903944085	75.4189	63	1137	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA11358;g__UBA11358	95.0	99.64	99.63	0.93	0.93	3	-
GCA_903845125.1	s__CAIMWS01 sp903845125	75.3367	74	1137	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1319;g__CAIMWS01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 17:37:51,561] [INFO] GTDB search result was written to GCA_018969165.1_ASM1896916v1_genomic.fna/result_gtdb.tsv
[2023-06-18 17:37:51,561] [INFO] ===== GTDB Search completed =====
[2023-06-18 17:37:51,570] [INFO] DFAST_QC result json was written to GCA_018969165.1_ASM1896916v1_genomic.fna/dqc_result.json
[2023-06-18 17:37:51,570] [INFO] DFAST_QC completed!
[2023-06-18 17:37:51,570] [INFO] Total running time: 0h2m31s