[2023-06-19 08:56:01,273] [INFO] DFAST_QC pipeline started.
[2023-06-19 08:56:01,275] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 08:56:01,275] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f6ab6de-342e-43c8-b2c7-687e7cfb2d0e/dqc_reference
[2023-06-19 08:56:02,503] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 08:56:02,504] [INFO] Task started: Prodigal
[2023-06-19 08:56:02,504] [INFO] Running command: gunzip -c /var/lib/cwl/stg0c74f838-1b8e-444c-98a1-d54d6410ca38/GCA_018609705.1_ASM1860970v1_genomic.fna.gz | prodigal -d GCA_018609705.1_ASM1860970v1_genomic.fna/cds.fna -a GCA_018609705.1_ASM1860970v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 08:56:13,579] [INFO] Task succeeded: Prodigal
[2023-06-19 08:56:13,580] [INFO] Task started: HMMsearch
[2023-06-19 08:56:13,580] [INFO] Running command: hmmsearch --tblout GCA_018609705.1_ASM1860970v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f6ab6de-342e-43c8-b2c7-687e7cfb2d0e/dqc_reference/reference_markers.hmm GCA_018609705.1_ASM1860970v1_genomic.fna/protein.faa > /dev/null
[2023-06-19 08:56:13,791] [INFO] Task succeeded: HMMsearch
[2023-06-19 08:56:13,792] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg0c74f838-1b8e-444c-98a1-d54d6410ca38/GCA_018609705.1_ASM1860970v1_genomic.fna.gz]
[2023-06-19 08:56:13,820] [INFO] Query marker FASTA was written to GCA_018609705.1_ASM1860970v1_genomic.fna/markers.fasta
[2023-06-19 08:56:13,821] [INFO] Task started: Blastn
[2023-06-19 08:56:13,821] [INFO] Running command: blastn -query GCA_018609705.1_ASM1860970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f6ab6de-342e-43c8-b2c7-687e7cfb2d0e/dqc_reference/reference_markers.fasta -out GCA_018609705.1_ASM1860970v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:56:14,394] [INFO] Task succeeded: Blastn
[2023-06-19 08:56:14,399] [INFO] Selected 10 target genomes.
[2023-06-19 08:56:14,399] [INFO] Target genome list was writen to GCA_018609705.1_ASM1860970v1_genomic.fna/target_genomes.txt
[2023-06-19 08:56:14,405] [INFO] Task started: fastANI
[2023-06-19 08:56:14,405] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c74f838-1b8e-444c-98a1-d54d6410ca38/GCA_018609705.1_ASM1860970v1_genomic.fna.gz --refList GCA_018609705.1_ASM1860970v1_genomic.fna/target_genomes.txt --output GCA_018609705.1_ASM1860970v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 08:56:19,980] [INFO] Task succeeded: fastANI
[2023-06-19 08:56:19,981] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f6ab6de-342e-43c8-b2c7-687e7cfb2d0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 08:56:19,981] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f6ab6de-342e-43c8-b2c7-687e7cfb2d0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 08:56:19,992] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 08:56:19,993] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-19 08:56:19,993] [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
Halovenus carboxidivorans	strain=WSH3	GCA_009831575.1	2692199	2692199	type	True	77.484	174	604	95	below_threshold
Halomicroarcula salina	strain=JCM 18369	GCA_019061225.1	1429914	1429914	type	True	77.3933	183	604	95	below_threshold
Halomicroarcula salina	strain=YGHS18	GCA_010119195.1	1429914	1429914	type	True	77.3298	184	604	95	below_threshold
Halomicroarcula limicola	strain=YGHS32	GCA_010119205.1	1429915	1429915	type	True	77.2337	201	604	95	below_threshold
Halomicrobium katesii	strain=DSM 19301	GCA_000379085.1	437163	437163	type	True	77.0093	165	604	95	below_threshold
Halomicrobium mukohataei	strain=DSM 12286	GCA_000023965.1	57705	57705	type	True	76.9482	173	604	95	below_threshold
Halobiforma haloterrestris	strain=DSM 13078	GCA_900112205.1	148448	148448	type	True	76.5572	127	604	95	below_threshold
Halobiforma lacisalsi	strain=AJ5	GCA_000336655.1	229731	229731	type	True	76.522	127	604	95	below_threshold
Halobiforma lacisalsi	strain=AJ5	GCA_000226975.3	229731	229731	type	True	76.4887	124	604	95	below_threshold
Natrialba hulunbeirensis	strain=JCM 10989	GCA_000337575.1	123783	123783	type	True	76.2293	109	604	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-19 08:56:19,995] [INFO] DFAST Taxonomy check result was written to GCA_018609705.1_ASM1860970v1_genomic.fna/tc_result.tsv
[2023-06-19 08:56:19,996] [INFO] ===== Taxonomy check completed =====
[2023-06-19 08:56:19,996] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 08:56:19,996] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f6ab6de-342e-43c8-b2c7-687e7cfb2d0e/dqc_reference/checkm_data
[2023-06-19 08:56:19,997] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 08:56:20,021] [INFO] Task started: CheckM
[2023-06-19 08:56:20,021] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018609705.1_ASM1860970v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018609705.1_ASM1860970v1_genomic.fna/checkm_input GCA_018609705.1_ASM1860970v1_genomic.fna/checkm_result
[2023-06-19 08:56:54,496] [INFO] Task succeeded: CheckM
[2023-06-19 08:56:54,498] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 24.22%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 08:56:54,518] [INFO] ===== Completeness check finished =====
[2023-06-19 08:56:54,518] [INFO] ===== Start GTDB Search =====
[2023-06-19 08:56:54,519] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018609705.1_ASM1860970v1_genomic.fna/markers.fasta)
[2023-06-19 08:56:54,519] [INFO] Task started: Blastn
[2023-06-19 08:56:54,519] [INFO] Running command: blastn -query GCA_018609705.1_ASM1860970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f6ab6de-342e-43c8-b2c7-687e7cfb2d0e/dqc_reference/reference_markers_gtdb.fasta -out GCA_018609705.1_ASM1860970v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 08:56:55,169] [INFO] Task succeeded: Blastn
[2023-06-19 08:56:55,175] [INFO] Selected 10 target genomes.
[2023-06-19 08:56:55,175] [INFO] Target genome list was writen to GCA_018609705.1_ASM1860970v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 08:56:55,204] [INFO] Task started: fastANI
[2023-06-19 08:56:55,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg0c74f838-1b8e-444c-98a1-d54d6410ca38/GCA_018609705.1_ASM1860970v1_genomic.fna.gz --refList GCA_018609705.1_ASM1860970v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018609705.1_ASM1860970v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 08:57:00,293] [INFO] Task succeeded: fastANI
[2023-06-19 08:57:00,308] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-19 08:57:00,308] [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_009789175.1	s__Salinibaculum litoreum	78.9827	265	604	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Salinibaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009831575.1	s__Halovenus sp009831575	77.4846	174	604	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halovenus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021655.1	s__QS-4-69-31 sp003021655	77.3361	157	604	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__QS-4-69-31	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003022725.1	s__Halovenus sp003022725	77.0657	143	604	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halovenus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009617995.1	s__Halomicrobium sp009617995	77.04	175	604	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicrobium	95.0	97.14	97.11	0.87	0.86	3	-
GCF_000379085.1	s__Halomicrobium katesii	76.9946	166	604	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicrobium	96.8107	N/A	N/A	N/A	N/A	1	-
GCA_003021285.1	s__Halovenus sp003021285	76.9901	112	604	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halovenus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021015.1	s__Halovenus sp003021015	76.9218	148	604	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halovenus	95.0	96.48	96.48	0.87	0.87	2	-
GCF_900112205.1	s__Halobiforma haloterrestris	76.5406	128	604	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	76.472	125	604	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.4693	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-19 08:57:00,311] [INFO] GTDB search result was written to GCA_018609705.1_ASM1860970v1_genomic.fna/result_gtdb.tsv
[2023-06-19 08:57:00,312] [INFO] ===== GTDB Search completed =====
[2023-06-19 08:57:00,318] [INFO] DFAST_QC result json was written to GCA_018609705.1_ASM1860970v1_genomic.fna/dqc_result.json
[2023-06-19 08:57:00,318] [INFO] DFAST_QC completed!
[2023-06-19 08:57:00,318] [INFO] Total running time: 0h0m59s