[2024-01-25 17:48:05,694] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:48:05,695] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:48:05,695] [INFO] DQC Reference Directory: /var/lib/cwl/stg9187dffd-4aac-40d6-92c0-533a922c0556/dqc_reference
[2024-01-25 17:48:06,934] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:48:06,935] [INFO] Task started: Prodigal
[2024-01-25 17:48:06,935] [INFO] Running command: gunzip -c /var/lib/cwl/stge4f4dac1-c33a-4fc8-a163-2a6b61b7a42b/GCF_902726645.1_Q1234_genomic.fna.gz | prodigal -d GCF_902726645.1_Q1234_genomic.fna/cds.fna -a GCF_902726645.1_Q1234_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:48:15,622] [INFO] Task succeeded: Prodigal
[2024-01-25 17:48:15,623] [INFO] Task started: HMMsearch
[2024-01-25 17:48:15,623] [INFO] Running command: hmmsearch --tblout GCF_902726645.1_Q1234_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9187dffd-4aac-40d6-92c0-533a922c0556/dqc_reference/reference_markers.hmm GCF_902726645.1_Q1234_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:48:15,868] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:48:15,869] [INFO] Found 6/6 markers.
[2024-01-25 17:48:15,905] [INFO] Query marker FASTA was written to GCF_902726645.1_Q1234_genomic.fna/markers.fasta
[2024-01-25 17:48:15,905] [INFO] Task started: Blastn
[2024-01-25 17:48:15,905] [INFO] Running command: blastn -query GCF_902726645.1_Q1234_genomic.fna/markers.fasta -db /var/lib/cwl/stg9187dffd-4aac-40d6-92c0-533a922c0556/dqc_reference/reference_markers.fasta -out GCF_902726645.1_Q1234_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:16,460] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:16,463] [INFO] Selected 30 target genomes.
[2024-01-25 17:48:16,464] [INFO] Target genome list was writen to GCF_902726645.1_Q1234_genomic.fna/target_genomes.txt
[2024-01-25 17:48:16,510] [INFO] Task started: fastANI
[2024-01-25 17:48:16,510] [INFO] Running command: fastANI --query /var/lib/cwl/stge4f4dac1-c33a-4fc8-a163-2a6b61b7a42b/GCF_902726645.1_Q1234_genomic.fna.gz --refList GCF_902726645.1_Q1234_genomic.fna/target_genomes.txt --output GCF_902726645.1_Q1234_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:48:38,018] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:38,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9187dffd-4aac-40d6-92c0-533a922c0556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:48:38,019] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9187dffd-4aac-40d6-92c0-533a922c0556/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:48:38,029] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:48:38,029] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:48:38,029] [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
Halobacillus ihumii	strain=Marseille-Q1234	GCA_902726645.1	2686092	2686092	type	True	100.0	1443	1445	95	conclusive
Halobacillus massiliensis	strain=Marseille-P3554	GCA_900166625.1	1926286	1926286	type	True	78.9556	168	1445	95	below_threshold
Virgibacillus doumboii	strain=Marseille-Q1616	GCA_902806455.1	2697503	2697503	type	True	78.9539	70	1445	95	below_threshold
Metabacillus schmidteae	strain=Marseille-P9898	GCA_903166545.1	2730405	2730405	type	True	78.6009	59	1445	95	below_threshold
Halobacillus karajensis	strain=DSM 14948	GCA_900108515.1	195088	195088	type	True	78.3989	174	1445	95	below_threshold
Virgibacillus dakarensis	strain=Marseille-P3469	GCA_900155625.1	1917889	1917889	type	True	78.0423	52	1445	95	below_threshold
Halobacillus andaensis	strain=CGMCC 1.12153	GCA_014636475.1	1176239	1176239	type	True	78.0265	207	1445	95	below_threshold
Halobacillus andaensis	strain=DSM 25866	GCA_017874135.1	1176239	1176239	type	True	78.0107	212	1445	95	below_threshold
Halobacillus kuroshimensis	strain=DSM 18393	GCA_000425705.1	302481	302481	type	True	77.9824	125	1445	95	below_threshold
Halobacillus litoralis	strain=SL-4	GCA_009856445.1	45668	45668	suspected-type	True	77.6041	166	1445	95	below_threshold
Salimicrobium halophilum	strain=DSM 4771	GCA_900100295.1	86666	86666	type	True	77.5608	57	1445	95	below_threshold
Sediminibacillus halophilus	strain=CGMCC 1.6199	GCA_900103695.1	482461	482461	type	True	77.1568	52	1445	95	below_threshold
Virgibacillus subterraneus	strain=CGMCC 1.7734	GCA_900110695.1	621109	621109	type	True	76.9474	63	1445	95	below_threshold
Virgibacillus oceani	strain=CGMCC 1.12754	GCA_014638995.1	1479511	1479511	type	True	76.7911	63	1445	95	below_threshold
Pontibacillus litoralis	strain=JSM 072002	GCA_000775615.1	516703	516703	type	True	76.5265	57	1445	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:48:38,031] [INFO] DFAST Taxonomy check result was written to GCF_902726645.1_Q1234_genomic.fna/tc_result.tsv
[2024-01-25 17:48:38,032] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:48:38,033] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:48:38,033] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9187dffd-4aac-40d6-92c0-533a922c0556/dqc_reference/checkm_data
[2024-01-25 17:48:38,034] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:48:38,078] [INFO] Task started: CheckM
[2024-01-25 17:48:38,078] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_902726645.1_Q1234_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_902726645.1_Q1234_genomic.fna/checkm_input GCF_902726645.1_Q1234_genomic.fna/checkm_result
[2024-01-25 17:49:08,403] [INFO] Task succeeded: CheckM
[2024-01-25 17:49:08,404] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:49:08,426] [INFO] ===== Completeness check finished =====
[2024-01-25 17:49:08,426] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:49:08,426] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_902726645.1_Q1234_genomic.fna/markers.fasta)
[2024-01-25 17:49:08,427] [INFO] Task started: Blastn
[2024-01-25 17:49:08,427] [INFO] Running command: blastn -query GCF_902726645.1_Q1234_genomic.fna/markers.fasta -db /var/lib/cwl/stg9187dffd-4aac-40d6-92c0-533a922c0556/dqc_reference/reference_markers_gtdb.fasta -out GCF_902726645.1_Q1234_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:49:09,264] [INFO] Task succeeded: Blastn
[2024-01-25 17:49:09,267] [INFO] Selected 23 target genomes.
[2024-01-25 17:49:09,267] [INFO] Target genome list was writen to GCF_902726645.1_Q1234_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:49:09,290] [INFO] Task started: fastANI
[2024-01-25 17:49:09,290] [INFO] Running command: fastANI --query /var/lib/cwl/stge4f4dac1-c33a-4fc8-a163-2a6b61b7a42b/GCF_902726645.1_Q1234_genomic.fna.gz --refList GCF_902726645.1_Q1234_genomic.fna/target_genomes_gtdb.txt --output GCF_902726645.1_Q1234_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:49:28,400] [INFO] Task succeeded: fastANI
[2024-01-25 17:49:28,410] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:49:28,411] [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
GCF_902726645.1	s__Halobacillus_A ihumii	100.0	1443	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900166655.1	s__Halobacillus_A hunanensis	94.0288	1212	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900166625.1	s__Halobacillus_A massiliensis	78.7317	167	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009858175.1	s__Pontibacillus sp009858175	78.5058	80	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108515.1	s__Halobacillus karajensis	78.401	175	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	99.38	99.37	0.93	0.93	4	-
GCF_002097535.1	s__Halobacillus mangrovi	78.0744	192	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014636475.1	s__Halobacillus_A andaensis	78.0443	206	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016908235.1	s__Halobacillus_A seohaensis	78.0162	221	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425705.1	s__Halobacillus kuroshimensis	77.9824	125	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	98.79	98.79	0.92	0.92	2	-
GCF_015905325.1	s__Halobacillus sp015905325	77.8561	140	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900240285.1	s__Halobacillus_A sp900240285	77.7159	199	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009856445.1	s__Halobacillus litoralis	77.6265	165	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Halobacillus	95.0	95.88	95.88	0.90	0.90	2	-
GCF_000425225.1	s__Pontibacillus marinus	76.8177	79	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014638995.1	s__Virgibacillus_E oceani	76.7496	67	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Virgibacillus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009856295.1	s__Pontibacillus yanchengensis_A	76.6778	70	1445	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Halobacillaceae;g__Pontibacillus	95.0	99.50	99.50	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-25 17:49:28,415] [INFO] GTDB search result was written to GCF_902726645.1_Q1234_genomic.fna/result_gtdb.tsv
[2024-01-25 17:49:28,416] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:49:28,420] [INFO] DFAST_QC result json was written to GCF_902726645.1_Q1234_genomic.fna/dqc_result.json
[2024-01-25 17:49:28,420] [INFO] DFAST_QC completed!
[2024-01-25 17:49:28,420] [INFO] Total running time: 0h1m23s