[2024-01-24 13:09:51,412] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:51,423] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:51,423] [INFO] DQC Reference Directory: /var/lib/cwl/stg11b039b3-141d-424d-b875-2f88bb0e6630/dqc_reference
[2024-01-24 13:09:52,914] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:52,915] [INFO] Task started: Prodigal
[2024-01-24 13:09:52,915] [INFO] Running command: gunzip -c /var/lib/cwl/stg06e551c6-729a-4b5b-9ef9-424a7ff37eab/GCF_024498195.1_ASM2449819v1_genomic.fna.gz | prodigal -d GCF_024498195.1_ASM2449819v1_genomic.fna/cds.fna -a GCF_024498195.1_ASM2449819v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:10:11,717] [INFO] Task succeeded: Prodigal
[2024-01-24 13:10:11,718] [INFO] Task started: HMMsearch
[2024-01-24 13:10:11,718] [INFO] Running command: hmmsearch --tblout GCF_024498195.1_ASM2449819v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg11b039b3-141d-424d-b875-2f88bb0e6630/dqc_reference/reference_markers.hmm GCF_024498195.1_ASM2449819v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:10:11,988] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:10:11,989] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg06e551c6-729a-4b5b-9ef9-424a7ff37eab/GCF_024498195.1_ASM2449819v1_genomic.fna.gz]
[2024-01-24 13:10:12,020] [INFO] Query marker FASTA was written to GCF_024498195.1_ASM2449819v1_genomic.fna/markers.fasta
[2024-01-24 13:10:12,020] [INFO] Task started: Blastn
[2024-01-24 13:10:12,021] [INFO] Running command: blastn -query GCF_024498195.1_ASM2449819v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11b039b3-141d-424d-b875-2f88bb0e6630/dqc_reference/reference_markers.fasta -out GCF_024498195.1_ASM2449819v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:12,545] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:12,548] [INFO] Selected 10 target genomes.
[2024-01-24 13:10:12,549] [INFO] Target genome list was writen to GCF_024498195.1_ASM2449819v1_genomic.fna/target_genomes.txt
[2024-01-24 13:10:12,553] [INFO] Task started: fastANI
[2024-01-24 13:10:12,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg06e551c6-729a-4b5b-9ef9-424a7ff37eab/GCF_024498195.1_ASM2449819v1_genomic.fna.gz --refList GCF_024498195.1_ASM2449819v1_genomic.fna/target_genomes.txt --output GCF_024498195.1_ASM2449819v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:10:22,069] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:22,070] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg11b039b3-141d-424d-b875-2f88bb0e6630/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:10:22,070] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg11b039b3-141d-424d-b875-2f88bb0e6630/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:10:22,089] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:10:22,089] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:10:22,090] [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
Halovivax cerinus	strain=IBRC-M 10256	GCA_024498195.1	1487865	1487865	type	True	100.0	1300	1300	95	conclusive
Halovivax ruber	strain=XH-70	GCA_000328525.1	387341	387341	type	True	84.2856	795	1300	95	below_threshold
Halovivax asiaticus	strain=JCM 14624	GCA_000337515.1	332953	332953	type	True	84.1512	776	1300	95	below_threshold
Halovivax limisalsi	strain=IBRC-M 10022	GCA_023093535.1	1453760	1453760	type	True	81.6876	725	1300	95	below_threshold
Haloterrigena alkaliphila	strain=KZCA68	GCA_017352155.2	2816475	2816475	type	True	78.457	476	1300	95	below_threshold
Halobiforma lacisalsi	strain=AJ5	GCA_000336655.1	229731	229731	type	True	78.2044	478	1300	95	below_threshold
Halobiforma lacisalsi	strain=AJ5	GCA_000226975.3	229731	229731	type	True	78.1891	485	1300	95	below_threshold
Natrinema salaciae	strain=DSM 25055	GCA_900110865.1	1186196	1186196	type	True	78.1787	459	1300	95	below_threshold
Halobiforma haloterrestris	strain=DSM 13078	GCA_900112205.1	148448	148448	type	True	78.1595	484	1300	95	below_threshold
Halostagnicola kamekurae	strain=DSM 22427	GCA_900116205.1	619731	619731	type	True	78.0217	368	1300	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:10:22,092] [INFO] DFAST Taxonomy check result was written to GCF_024498195.1_ASM2449819v1_genomic.fna/tc_result.tsv
[2024-01-24 13:10:22,094] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:10:22,094] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:10:22,094] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg11b039b3-141d-424d-b875-2f88bb0e6630/dqc_reference/checkm_data
[2024-01-24 13:10:22,097] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:10:22,153] [INFO] Task started: CheckM
[2024-01-24 13:10:22,153] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024498195.1_ASM2449819v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024498195.1_ASM2449819v1_genomic.fna/checkm_input GCF_024498195.1_ASM2449819v1_genomic.fna/checkm_result
[2024-01-24 13:11:14,032] [INFO] Task succeeded: CheckM
[2024-01-24 13:11:14,034] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:11:14,051] [INFO] ===== Completeness check finished =====
[2024-01-24 13:11:14,052] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:11:14,052] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024498195.1_ASM2449819v1_genomic.fna/markers.fasta)
[2024-01-24 13:11:14,053] [INFO] Task started: Blastn
[2024-01-24 13:11:14,053] [INFO] Running command: blastn -query GCF_024498195.1_ASM2449819v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg11b039b3-141d-424d-b875-2f88bb0e6630/dqc_reference/reference_markers_gtdb.fasta -out GCF_024498195.1_ASM2449819v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:11:14,580] [INFO] Task succeeded: Blastn
[2024-01-24 13:11:14,584] [INFO] Selected 13 target genomes.
[2024-01-24 13:11:14,584] [INFO] Target genome list was writen to GCF_024498195.1_ASM2449819v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:11:14,594] [INFO] Task started: fastANI
[2024-01-24 13:11:14,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg06e551c6-729a-4b5b-9ef9-424a7ff37eab/GCF_024498195.1_ASM2449819v1_genomic.fna.gz --refList GCF_024498195.1_ASM2449819v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024498195.1_ASM2449819v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:11:25,001] [INFO] Task succeeded: fastANI
[2024-01-24 13:11:25,019] [INFO] Found 13 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:11:25,019] [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_000328525.1	s__Halovivax ruber	84.25	798	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halovivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337515.1	s__Halovivax asiaticus	84.1762	774	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halovivax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352155.1	s__Haloterrigena sp017352155	78.5595	455	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017357405.1	s__KZCA124 sp017357405	78.2474	464	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__KZCA124	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100335.1	s__Natronorubrum texcoconense	78.2271	443	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112205.1	s__Halobiforma haloterrestris	78.1878	481	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.4693	N/A	N/A	N/A	N/A	1	-
GCF_000226975.2	s__Halobiforma lacisalsi	78.1818	486	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.4693	99.98	99.98	1.00	1.00	2	-
GCF_900110865.1	s__Natrinema salaciae	78.1728	462	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002572525.1	s__Natrinema sp002572525	78.1614	426	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003559215.1	s__Natronococcus sp003559215	78.1005	444	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	99.83	99.81	0.98	0.98	4	-
GCF_003841505.1	s__Natrarchaeobius chitinivorans	78.0094	394	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116205.1	s__Halostagnicola kamekurae	78.0041	372	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halostagnicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834785.1	s__Natronorubrum halalkaliphilum	77.9891	398	1300	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:11:25,020] [INFO] GTDB search result was written to GCF_024498195.1_ASM2449819v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:11:25,021] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:11:25,025] [INFO] DFAST_QC result json was written to GCF_024498195.1_ASM2449819v1_genomic.fna/dqc_result.json
[2024-01-24 13:11:25,025] [INFO] DFAST_QC completed!
[2024-01-24 13:11:25,025] [INFO] Total running time: 0h1m34s