[2023-06-18 18:10:29,935] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:10:29,938] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:10:29,938] [INFO] DQC Reference Directory: /var/lib/cwl/stge052be01-f42c-4dd9-a364-89525315ebde/dqc_reference
[2023-06-18 18:10:31,280] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:10:31,281] [INFO] Task started: Prodigal
[2023-06-18 18:10:31,282] [INFO] Running command: gunzip -c /var/lib/cwl/stg61c872c5-a9b9-4130-8ef0-ec089175192d/GCA_029554425.1_ASM2955442v1_genomic.fna.gz | prodigal -d GCA_029554425.1_ASM2955442v1_genomic.fna/cds.fna -a GCA_029554425.1_ASM2955442v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:10:53,180] [INFO] Task succeeded: Prodigal
[2023-06-18 18:10:53,181] [INFO] Task started: HMMsearch
[2023-06-18 18:10:53,181] [INFO] Running command: hmmsearch --tblout GCA_029554425.1_ASM2955442v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge052be01-f42c-4dd9-a364-89525315ebde/dqc_reference/reference_markers.hmm GCA_029554425.1_ASM2955442v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:10:53,452] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:10:53,455] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg61c872c5-a9b9-4130-8ef0-ec089175192d/GCA_029554425.1_ASM2955442v1_genomic.fna.gz]
[2023-06-18 18:10:53,500] [INFO] Query marker FASTA was written to GCA_029554425.1_ASM2955442v1_genomic.fna/markers.fasta
[2023-06-18 18:10:53,501] [INFO] Task started: Blastn
[2023-06-18 18:10:53,501] [INFO] Running command: blastn -query GCA_029554425.1_ASM2955442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge052be01-f42c-4dd9-a364-89525315ebde/dqc_reference/reference_markers.fasta -out GCA_029554425.1_ASM2955442v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:10:54,152] [INFO] Task succeeded: Blastn
[2023-06-18 18:10:54,159] [INFO] Selected 13 target genomes.
[2023-06-18 18:10:54,160] [INFO] Target genome list was writen to GCA_029554425.1_ASM2955442v1_genomic.fna/target_genomes.txt
[2023-06-18 18:10:54,161] [INFO] Task started: fastANI
[2023-06-18 18:10:54,161] [INFO] Running command: fastANI --query /var/lib/cwl/stg61c872c5-a9b9-4130-8ef0-ec089175192d/GCA_029554425.1_ASM2955442v1_genomic.fna.gz --refList GCA_029554425.1_ASM2955442v1_genomic.fna/target_genomes.txt --output GCA_029554425.1_ASM2955442v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:11:03,489] [INFO] Task succeeded: fastANI
[2023-06-18 18:11:03,490] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge052be01-f42c-4dd9-a364-89525315ebde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:11:03,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge052be01-f42c-4dd9-a364-89525315ebde/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:11:03,514] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 18:11:03,514] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 18:11:03,514] [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
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	77.5987	215	974	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	77.5038	166	974	95	below_threshold
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	77.4775	164	974	95	below_threshold
Cephaloticoccus primus	strain=CAG34	GCA_001580015.1	1548207	1548207	type	True	77.2267	112	974	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	77.0425	145	974	95	below_threshold
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	77.0327	204	974	95	below_threshold
Actinomadura barringtoniae	strain=GKU 128	GCA_017573505.1	1427535	1427535	type	True	74.752	88	974	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 18:11:03,517] [INFO] DFAST Taxonomy check result was written to GCA_029554425.1_ASM2955442v1_genomic.fna/tc_result.tsv
[2023-06-18 18:11:03,517] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:11:03,517] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:11:03,518] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge052be01-f42c-4dd9-a364-89525315ebde/dqc_reference/checkm_data
[2023-06-18 18:11:03,519] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:11:03,556] [INFO] Task started: CheckM
[2023-06-18 18:11:03,556] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_029554425.1_ASM2955442v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_029554425.1_ASM2955442v1_genomic.fna/checkm_input GCA_029554425.1_ASM2955442v1_genomic.fna/checkm_result
[2023-06-18 18:12:03,031] [INFO] Task succeeded: CheckM
[2023-06-18 18:12:03,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 18:12:03,062] [INFO] ===== Completeness check finished =====
[2023-06-18 18:12:03,063] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:12:03,063] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_029554425.1_ASM2955442v1_genomic.fna/markers.fasta)
[2023-06-18 18:12:03,063] [INFO] Task started: Blastn
[2023-06-18 18:12:03,064] [INFO] Running command: blastn -query GCA_029554425.1_ASM2955442v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge052be01-f42c-4dd9-a364-89525315ebde/dqc_reference/reference_markers_gtdb.fasta -out GCA_029554425.1_ASM2955442v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:12:04,129] [INFO] Task succeeded: Blastn
[2023-06-18 18:12:04,136] [INFO] Selected 19 target genomes.
[2023-06-18 18:12:04,137] [INFO] Target genome list was writen to GCA_029554425.1_ASM2955442v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:12:04,141] [INFO] Task started: fastANI
[2023-06-18 18:12:04,141] [INFO] Running command: fastANI --query /var/lib/cwl/stg61c872c5-a9b9-4130-8ef0-ec089175192d/GCA_029554425.1_ASM2955442v1_genomic.fna.gz --refList GCA_029554425.1_ASM2955442v1_genomic.fna/target_genomes_gtdb.txt --output GCA_029554425.1_ASM2955442v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:12:16,815] [INFO] Task succeeded: fastANI
[2023-06-18 18:12:16,830] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:12:16,830] [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_002070825.1	s__MWDT01 sp002070825	97.1352	447	974	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__MWDT01	95.0	97.04	96.87	0.67	0.67	3	conclusive
GCA_016217595.1	s__MWDT01 sp016217595	79.0069	207	974	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__MWDT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016715765.1	s__UBA2377 sp016715765	78.0835	186	974	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA2377	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839035.1	s__Opi-474 sp903839035	77.9117	179	974	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.67	99.48	0.93	0.89	8	-
GCA_903881475.1	s__Opi-474 sp903881475	77.8345	181	974	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.50	98.31	0.92	0.83	9	-
GCA_903872505.1	s__Opi-474 sp903872505	77.7954	201	974	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.99	99.98	0.99	0.99	3	-
GCA_903902745.1	s__CAIUWA01 sp903902745	77.7764	169	974	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAIUWA01	95.0	99.98	99.98	0.98	0.97	4	-
GCA_903855985.1	s__Opi-474 sp903855985	77.6637	190	974	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.84	99.84	0.94	0.94	2	-
GCA_903859715.1	s__Opi-474 sp903859715	77.6499	167	974	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.98	99.96	0.98	0.96	7	-
GCA_016235555.1	s__ER46 sp016235555	77.6301	253	974	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016187945.1	s__Didemnitutus sp016187945	77.6212	222	974	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Didemnitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879845.1	s__J108 sp014879845	77.6173	198	974	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__J108	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000242935.3	s__Geminisphaera sp000242935	77.6054	235	974	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Geminisphaera	95.0	96.61	96.61	0.73	0.73	2	-
GCA_903898675.1	s__Lacunisphaera sp903898675	77.317	163	974	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	99.99	99.98	0.99	0.98	5	-
GCA_016871755.1	s__UBA6669 sp016871755	77.2779	125	974	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA6669	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018239675.1	s__Opi-474 sp018239675	77.1657	179	974	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903862595.1	s__UBA6669 sp903862595	76.9168	113	974	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA6669	95.0	99.22	99.13	0.81	0.80	3	-
GCA_009695305.1	s__CAITWF01 sp009695305	76.8823	162	974	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAITWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003694825.1	s__J108 sp003694825	76.3092	101	974	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__J108	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 18:12:16,833] [INFO] GTDB search result was written to GCA_029554425.1_ASM2955442v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:12:16,835] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:12:16,841] [INFO] DFAST_QC result json was written to GCA_029554425.1_ASM2955442v1_genomic.fna/dqc_result.json
[2023-06-18 18:12:16,841] [INFO] DFAST_QC completed!
[2023-06-18 18:12:16,841] [INFO] Total running time: 0h1m47s