[2023-06-29 13:25:13,953] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:25:13,959] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:25:13,959] [INFO] DQC Reference Directory: /var/lib/cwl/stg77b13b07-9a80-4f82-84da-531f9eba82b2/dqc_reference
[2023-06-29 13:25:15,229] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:25:15,230] [INFO] Task started: Prodigal
[2023-06-29 13:25:15,231] [INFO] Running command: gunzip -c /var/lib/cwl/stg311f9bac-a150-4d62-af8b-cefab570bcd2/GCA_023446615.1_ASM2344661v1_genomic.fna.gz | prodigal -d GCA_023446615.1_ASM2344661v1_genomic.fna/cds.fna -a GCA_023446615.1_ASM2344661v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:25:46,218] [INFO] Task succeeded: Prodigal
[2023-06-29 13:25:46,218] [INFO] Task started: HMMsearch
[2023-06-29 13:25:46,218] [INFO] Running command: hmmsearch --tblout GCA_023446615.1_ASM2344661v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77b13b07-9a80-4f82-84da-531f9eba82b2/dqc_reference/reference_markers.hmm GCA_023446615.1_ASM2344661v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:25:46,506] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:25:46,508] [INFO] Found 6/6 markers.
[2023-06-29 13:25:46,554] [INFO] Query marker FASTA was written to GCA_023446615.1_ASM2344661v1_genomic.fna/markers.fasta
[2023-06-29 13:25:46,554] [INFO] Task started: Blastn
[2023-06-29 13:25:46,555] [INFO] Running command: blastn -query GCA_023446615.1_ASM2344661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77b13b07-9a80-4f82-84da-531f9eba82b2/dqc_reference/reference_markers.fasta -out GCA_023446615.1_ASM2344661v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:25:47,264] [INFO] Task succeeded: Blastn
[2023-06-29 13:25:47,269] [INFO] Selected 9 target genomes.
[2023-06-29 13:25:47,270] [INFO] Target genome list was writen to GCA_023446615.1_ASM2344661v1_genomic.fna/target_genomes.txt
[2023-06-29 13:25:47,273] [INFO] Task started: fastANI
[2023-06-29 13:25:47,273] [INFO] Running command: fastANI --query /var/lib/cwl/stg311f9bac-a150-4d62-af8b-cefab570bcd2/GCA_023446615.1_ASM2344661v1_genomic.fna.gz --refList GCA_023446615.1_ASM2344661v1_genomic.fna/target_genomes.txt --output GCA_023446615.1_ASM2344661v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:25:54,855] [INFO] Task succeeded: fastANI
[2023-06-29 13:25:54,855] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77b13b07-9a80-4f82-84da-531f9eba82b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:25:54,856] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77b13b07-9a80-4f82-84da-531f9eba82b2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:25:54,865] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:25:54,866] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 13:25:54,866] [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
Opitutus terrae	strain=PB90-1	GCA_000019965.1	107709	107709	type	True	77.1711	251	1525	95	below_threshold
Nibricoccus aquaticus	strain=HZ-65	GCA_002310495.1	2576891	2576891	type	True	76.9007	187	1525	95	below_threshold
Rariglobus hedericola	strain=53C-WASEF	GCA_007559335.1	2597822	2597822	type	True	76.8844	145	1525	95	below_threshold
Cephaloticoccus primus	strain=CAG34	GCA_001580015.1	1548207	1548207	type	True	76.8486	116	1525	95	below_threshold
Geminisphaera colitermitum	strain=TAV2	GCA_000171235.2	1148786	1148786	type	True	76.665	125	1525	95	below_threshold
Cephaloticoccus capnophilus	strain=CV41	GCA_001580045.1	1548208	1548208	type	True	76.6261	65	1525	95	below_threshold
Ereboglobus luteus	strain=Ho45	GCA_003096195.1	1796921	1796921	type	True	76.3583	113	1525	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 13:25:54,868] [INFO] DFAST Taxonomy check result was written to GCA_023446615.1_ASM2344661v1_genomic.fna/tc_result.tsv
[2023-06-29 13:25:54,869] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:25:54,869] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:25:54,870] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77b13b07-9a80-4f82-84da-531f9eba82b2/dqc_reference/checkm_data
[2023-06-29 13:25:54,872] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:25:54,922] [INFO] Task started: CheckM
[2023-06-29 13:25:54,922] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023446615.1_ASM2344661v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023446615.1_ASM2344661v1_genomic.fna/checkm_input GCA_023446615.1_ASM2344661v1_genomic.fna/checkm_result
[2023-06-29 13:27:17,982] [INFO] Task succeeded: CheckM
[2023-06-29 13:27:17,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:27:18,006] [INFO] ===== Completeness check finished =====
[2023-06-29 13:27:18,007] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:27:18,007] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023446615.1_ASM2344661v1_genomic.fna/markers.fasta)
[2023-06-29 13:27:18,007] [INFO] Task started: Blastn
[2023-06-29 13:27:18,008] [INFO] Running command: blastn -query GCA_023446615.1_ASM2344661v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77b13b07-9a80-4f82-84da-531f9eba82b2/dqc_reference/reference_markers_gtdb.fasta -out GCA_023446615.1_ASM2344661v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:27:19,207] [INFO] Task succeeded: Blastn
[2023-06-29 13:27:19,212] [INFO] Selected 25 target genomes.
[2023-06-29 13:27:19,213] [INFO] Target genome list was writen to GCA_023446615.1_ASM2344661v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:27:19,224] [INFO] Task started: fastANI
[2023-06-29 13:27:19,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg311f9bac-a150-4d62-af8b-cefab570bcd2/GCA_023446615.1_ASM2344661v1_genomic.fna.gz --refList GCA_023446615.1_ASM2344661v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023446615.1_ASM2344661v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:27:36,652] [INFO] Task succeeded: fastANI
[2023-06-29 13:27:36,675] [INFO] Found 25 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 13:27:36,676] [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_016871755.1	s__UBA6669 sp016871755	77.5887	196	1525	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__UBA6669	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903902745.1	s__CAIUWA01 sp903902745	77.5341	185	1525	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAIUWA01	95.0	99.98	99.98	0.98	0.97	4	-
GCA_903872505.1	s__Opi-474 sp903872505	77.4804	213	1525	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_903855985.1	s__Opi-474 sp903855985	77.4337	194	1525	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_900299415.1	s__CAIYFD01 sp900299415	77.4298	120	1525	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAIYFD01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903830425.1	s__Opi-474 sp903830425	77.351	228	1525	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opi-474	95.0	99.49	99.28	0.91	0.87	25	-
GCA_018239845.1	s__Opitutus sp018239845	77.3098	229	1525	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Opitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016793535.1	s__ER46 sp016793535	77.3007	235	1525	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003054705.1	s__ER46 sp003054705	77.2154	242	1525	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	77.1191	206	1525	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Didemnitutus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016222805.1	s__ER46 sp016222805	77.1122	210	1525	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001650175.1	s__Ereboglobus sp001650175	76.9799	171	1525	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Ereboglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003054665.1	s__EW11 sp003054665	76.9407	211	1525	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__EW11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016217595.1	s__MWDT01 sp016217595	76.859	148	1525	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__MWDT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903891325.1	s__Palsa-1447 sp903891325	76.8582	115	1525	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Palsa-1447	95.0	99.85	99.79	0.96	0.95	3	-
GCA_014879845.1	s__J108 sp014879845	76.8582	198	1525	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__J108	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016235555.1	s__ER46 sp016235555	76.8288	263	1525	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794785.1	s__ER46 sp016794785	76.7778	231	1525	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016794665.1	s__ER46 sp016794665	76.7776	200	1525	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__ER46	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903916755.1	s__Palsa-1447 sp903916755	76.7336	136	1525	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Palsa-1447	95.0	99.68	99.68	0.97	0.97	2	-
GCA_903873805.1	s__CAIQQB01 sp903873805	76.7081	178	1525	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__CAIQQB01	95.0	99.97	99.97	0.95	0.95	2	-
GCA_016795545.1	s__Lacunisphaera sp016795545	76.7071	201	1525	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Lacunisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016199925.1	s__JACQFT01 sp016199925	76.6453	155	1525	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__JACQFT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903885525.1	s__Didemnitutus sp903885525	76.2297	72	1525	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Opitutales;f__Opitutaceae;g__Didemnitutus	95.0	99.59	99.59	0.87	0.87	2	-
GCA_004143945.1	s__Dokdonella_A sp004143945	75.0075	57	1525	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dokdonella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:27:36,678] [INFO] GTDB search result was written to GCA_023446615.1_ASM2344661v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:27:36,678] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:27:36,682] [INFO] DFAST_QC result json was written to GCA_023446615.1_ASM2344661v1_genomic.fna/dqc_result.json
[2023-06-29 13:27:36,683] [INFO] DFAST_QC completed!
[2023-06-29 13:27:36,683] [INFO] Total running time: 0h2m23s