[2023-06-19 13:54:34,716] [INFO] DFAST_QC pipeline started.
[2023-06-19 13:54:34,717] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 13:54:34,717] [INFO] DQC Reference Directory: /var/lib/cwl/stge44c026e-8085-4749-91fc-45c8fe825d75/dqc_reference
[2023-06-19 13:54:35,844] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 13:54:35,844] [INFO] Task started: Prodigal
[2023-06-19 13:54:35,845] [INFO] Running command: gunzip -c /var/lib/cwl/stgda4572fd-6ea6-4edc-bbcd-136c69b0a03e/GCA_018821195.1_ASM1882119v1_genomic.fna.gz | prodigal -d GCA_018821195.1_ASM1882119v1_genomic.fna/cds.fna -a GCA_018821195.1_ASM1882119v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 13:54:46,760] [INFO] Task succeeded: Prodigal
[2023-06-19 13:54:46,760] [INFO] Task started: HMMsearch
[2023-06-19 13:54:46,760] [INFO] Running command: hmmsearch --tblout GCA_018821195.1_ASM1882119v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge44c026e-8085-4749-91fc-45c8fe825d75/dqc_reference/reference_markers.hmm GCA_018821195.1_ASM1882119v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 13:54:46,982] [INFO] Task succeeded: HMMsearch
[2023-06-19 13:54:46,983] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgda4572fd-6ea6-4edc-bbcd-136c69b0a03e/GCA_018821195.1_ASM1882119v1_genomic.fna.gz]
[2023-06-19 13:54:47,021] [INFO] Query marker FASTA was written to GCA_018821195.1_ASM1882119v1_genomic.fna/markers.fasta
[2023-06-19 13:54:47,021] [INFO] Task started: Blastn
[2023-06-19 13:54:47,021] [INFO] Running command: blastn -query GCA_018821195.1_ASM1882119v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge44c026e-8085-4749-91fc-45c8fe825d75/dqc_reference/reference_markers.fasta -out GCA_018821195.1_ASM1882119v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:54:47,700] [INFO] Task succeeded: Blastn
[2023-06-19 13:54:47,703] [INFO] Selected 31 target genomes.
[2023-06-19 13:54:47,703] [INFO] Target genome list was writen to GCA_018821195.1_ASM1882119v1_genomic.fna/target_genomes.txt
[2023-06-19 13:54:47,705] [INFO] Task started: fastANI
[2023-06-19 13:54:47,706] [INFO] Running command: fastANI --query /var/lib/cwl/stgda4572fd-6ea6-4edc-bbcd-136c69b0a03e/GCA_018821195.1_ASM1882119v1_genomic.fna.gz --refList GCA_018821195.1_ASM1882119v1_genomic.fna/target_genomes.txt --output GCA_018821195.1_ASM1882119v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 13:55:08,434] [INFO] Task succeeded: fastANI
[2023-06-19 13:55:08,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge44c026e-8085-4749-91fc-45c8fe825d75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 13:55:08,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge44c026e-8085-4749-91fc-45c8fe825d75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 13:55:08,442] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 13:55:08,443] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 13:55:08,443] [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
Arenimonas caeni	strain=z29	GCA_003024235.1	2058085	2058085	type	True	75.2398	61	1255	95	below_threshold
Arenimonas metalli	strain=CF5-1	GCA_000747155.1	948077	948077	type	True	75.213	53	1255	95	below_threshold
Haliangium ochraceum	strain=DSM 14365	GCA_000024805.1	80816	80816	type	True	75.211	127	1255	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	75.1818	56	1255	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	75.1298	63	1255	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	75.0914	88	1255	95	below_threshold
Myxococcus llanfairpwllgwyngyllgogerychwyrndrobwllllantysiliogogogochensis	strain=AM401	GCA_006636215.1	2590453	2590453	type	True	75.0016	83	1255	95	below_threshold
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.96	145	1255	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.9395	143	1255	95	below_threshold
Gordonia insulae	strain=MMS17-SY073	GCA_003855095.1	2420509	2420509	type	True	74.8146	51	1255	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	74.8146	81	1255	95	below_threshold
Paludisphaera rhizosphaereae	strain=JC665	GCA_011065895.1	2711216	2711216	type	True	74.6754	52	1255	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 13:55:08,444] [INFO] DFAST Taxonomy check result was written to GCA_018821195.1_ASM1882119v1_genomic.fna/tc_result.tsv
[2023-06-19 13:55:08,444] [INFO] ===== Taxonomy check completed =====
[2023-06-19 13:55:08,444] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 13:55:08,445] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge44c026e-8085-4749-91fc-45c8fe825d75/dqc_reference/checkm_data
[2023-06-19 13:55:08,445] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 13:55:08,487] [INFO] Task started: CheckM
[2023-06-19 13:55:08,487] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018821195.1_ASM1882119v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018821195.1_ASM1882119v1_genomic.fna/checkm_input GCA_018821195.1_ASM1882119v1_genomic.fna/checkm_result
[2023-06-19 13:55:44,906] [INFO] Task succeeded: CheckM
[2023-06-19 13:55:44,907] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 13:55:44,927] [INFO] ===== Completeness check finished =====
[2023-06-19 13:55:44,927] [INFO] ===== Start GTDB Search =====
[2023-06-19 13:55:44,927] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018821195.1_ASM1882119v1_genomic.fna/markers.fasta)
[2023-06-19 13:55:44,927] [INFO] Task started: Blastn
[2023-06-19 13:55:44,927] [INFO] Running command: blastn -query GCA_018821195.1_ASM1882119v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge44c026e-8085-4749-91fc-45c8fe825d75/dqc_reference/reference_markers_gtdb.fasta -out GCA_018821195.1_ASM1882119v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 13:55:46,002] [INFO] Task succeeded: Blastn
[2023-06-19 13:55:46,005] [INFO] Selected 18 target genomes.
[2023-06-19 13:55:46,005] [INFO] Target genome list was writen to GCA_018821195.1_ASM1882119v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 13:55:46,010] [INFO] Task started: fastANI
[2023-06-19 13:55:46,010] [INFO] Running command: fastANI --query /var/lib/cwl/stgda4572fd-6ea6-4edc-bbcd-136c69b0a03e/GCA_018821195.1_ASM1882119v1_genomic.fna.gz --refList GCA_018821195.1_ASM1882119v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018821195.1_ASM1882119v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 13:56:00,738] [INFO] Task succeeded: fastANI
[2023-06-19 13:56:00,745] [INFO] Found 11 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-19 13:56:00,745] [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_002841825.1	s__HGW-17 sp002841825	97.8421	995	1255	d__Bacteria;p__Myxococcota;c__Polyangia;o__HGW-17;f__HGW-17;g__HGW-17	95.0	97.98	97.84	0.81	0.78	4	inconclusive
GCA_018817795.1	s__HGW-17 sp018817795	95.1382	843	1255	d__Bacteria;p__Myxococcota;c__Polyangia;o__HGW-17;f__HGW-17;g__HGW-17	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCA_002841905.1	s__HGW-17 sp002841905	89.3669	592	1255	d__Bacteria;p__Myxococcota;c__Polyangia;o__HGW-17;f__HGW-17;g__HGW-17	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003249585.1	s__SZUA-580 sp003249585	77.2032	97	1255	d__Bacteria;p__Myxococcota;c__Polyangia;o__HGW-17;f__HGW-17;g__SZUA-580	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016709225.1	s__Ga0077550 sp016709225	75.2159	116	1255	d__Bacteria;p__Myxococcota;c__Polyangia;o__Nannocystales;f__Nannocystaceae;g__Ga0077550	95.0	99.66	99.17	0.98	0.94	4	-
GCA_900696455.1	s__UBA2376 sp900696455	75.1875	151	1255	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	98.40	97.29	0.91	0.90	3	-
GCA_006226565.1	s__PHBI01 sp006226565	75.1758	122	1255	d__Bacteria;p__Myxococcota;c__UBA9042;o__PHBI01;f__PHBI01;g__PHBI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903897935.1	s__CAIUDO01 sp903897935	75.15	62	1255	d__Bacteria;p__Myxococcota_A;c__UBA796;o__UBA796;f__GCA-2862545;g__CAIUDO01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526095.1	s__WYBA01 sp011526095	75.0058	145	1255	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__WYBA01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018069875.1	s__Ideonella sp018069875	74.9488	79	1255	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ideonella	95.0	98.74	98.74	0.92	0.92	2	-
GCF_011065895.1	s__Paludisphaera sp011065895	74.6764	52	1255	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Isosphaerales;f__Isosphaeraceae;g__Paludisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 13:56:00,747] [INFO] GTDB search result was written to GCA_018821195.1_ASM1882119v1_genomic.fna/result_gtdb.tsv
[2023-06-19 13:56:00,747] [INFO] ===== GTDB Search completed =====
[2023-06-19 13:56:00,750] [INFO] DFAST_QC result json was written to GCA_018821195.1_ASM1882119v1_genomic.fna/dqc_result.json
[2023-06-19 13:56:00,750] [INFO] DFAST_QC completed!
[2023-06-19 13:56:00,750] [INFO] Total running time: 0h1m26s