[2024-01-24 14:05:31,707] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:31,709] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:31,709] [INFO] DQC Reference Directory: /var/lib/cwl/stg14cb3d5f-eb16-42c7-bc65-6d02ed396f81/dqc_reference
[2024-01-24 14:05:32,946] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:32,947] [INFO] Task started: Prodigal
[2024-01-24 14:05:32,947] [INFO] Running command: gunzip -c /var/lib/cwl/stga7a267f3-8828-4637-80f9-dd1b95cf0b6c/GCF_020177375.1_ASM2017737v1_genomic.fna.gz | prodigal -d GCF_020177375.1_ASM2017737v1_genomic.fna/cds.fna -a GCF_020177375.1_ASM2017737v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:53,185] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:53,185] [INFO] Task started: HMMsearch
[2024-01-24 14:05:53,185] [INFO] Running command: hmmsearch --tblout GCF_020177375.1_ASM2017737v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg14cb3d5f-eb16-42c7-bc65-6d02ed396f81/dqc_reference/reference_markers.hmm GCF_020177375.1_ASM2017737v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:53,447] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:53,448] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga7a267f3-8828-4637-80f9-dd1b95cf0b6c/GCF_020177375.1_ASM2017737v1_genomic.fna.gz]
[2024-01-24 14:05:53,487] [INFO] Query marker FASTA was written to GCF_020177375.1_ASM2017737v1_genomic.fna/markers.fasta
[2024-01-24 14:05:53,487] [INFO] Task started: Blastn
[2024-01-24 14:05:53,487] [INFO] Running command: blastn -query GCF_020177375.1_ASM2017737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14cb3d5f-eb16-42c7-bc65-6d02ed396f81/dqc_reference/reference_markers.fasta -out GCF_020177375.1_ASM2017737v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:54,027] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:54,031] [INFO] Selected 11 target genomes.
[2024-01-24 14:05:54,031] [INFO] Target genome list was writen to GCF_020177375.1_ASM2017737v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:54,036] [INFO] Task started: fastANI
[2024-01-24 14:05:54,036] [INFO] Running command: fastANI --query /var/lib/cwl/stga7a267f3-8828-4637-80f9-dd1b95cf0b6c/GCF_020177375.1_ASM2017737v1_genomic.fna.gz --refList GCF_020177375.1_ASM2017737v1_genomic.fna/target_genomes.txt --output GCF_020177375.1_ASM2017737v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:04,305] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:04,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg14cb3d5f-eb16-42c7-bc65-6d02ed396f81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:04,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg14cb3d5f-eb16-42c7-bc65-6d02ed396f81/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:04,316] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:06:04,316] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:06:04,316] [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
Natronococcus jeotgali	strain=DSM 18795	GCA_000337695.1	413812	413812	type	True	80.0396	589	1470	95	below_threshold
Natronococcus amylolyticus	strain=DSM 10524	GCA_000337675.1	44470	44470	type	True	79.2904	550	1470	95	below_threshold
Haloterrigena alkaliphila	strain=KZCA68	GCA_017352155.2	2816475	2816475	type	True	79.1845	542	1470	95	below_threshold
Natronococcus occultus	strain=SP4	GCA_000328685.1	29288	29288	type	True	79.1071	575	1470	95	below_threshold
Halopiger salifodinae	strain=KCY07-B2	GCA_000784335.1	1202768	1202768	type	True	79.0655	537	1470	95	below_threshold
Halopiger salifodinae	strain=CGMCC 1.12284	GCA_900110455.1	1202768	1202768	type	True	79.0593	535	1470	95	below_threshold
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	78.9893	597	1470	95	below_threshold
Haloterrigena salina	strain=JCM 13891	GCA_000337495.1	504937	504937	type	True	78.9292	576	1470	95	below_threshold
Natronococcus pandeyae	strain=LS1_42	GCA_008122205.1	2055836	2055836	type	True	78.8812	540	1470	95	below_threshold
Haloterrigena salifodinae	strain=ZY19	GCA_003977755.1	2675099	2675099	type	True	78.6875	577	1470	95	below_threshold
Halovivax cerinus	strain=IBRC-M 10256	GCA_024498195.1	1487865	1487865	type	True	78.0866	376	1470	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:04,318] [INFO] DFAST Taxonomy check result was written to GCF_020177375.1_ASM2017737v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:04,319] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:04,319] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:04,319] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg14cb3d5f-eb16-42c7-bc65-6d02ed396f81/dqc_reference/checkm_data
[2024-01-24 14:06:04,320] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:04,380] [INFO] Task started: CheckM
[2024-01-24 14:06:04,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020177375.1_ASM2017737v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020177375.1_ASM2017737v1_genomic.fna/checkm_input GCF_020177375.1_ASM2017737v1_genomic.fna/checkm_result
[2024-01-24 14:07:01,541] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:01,543] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:01,562] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:01,562] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:01,562] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020177375.1_ASM2017737v1_genomic.fna/markers.fasta)
[2024-01-24 14:07:01,563] [INFO] Task started: Blastn
[2024-01-24 14:07:01,563] [INFO] Running command: blastn -query GCF_020177375.1_ASM2017737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg14cb3d5f-eb16-42c7-bc65-6d02ed396f81/dqc_reference/reference_markers_gtdb.fasta -out GCF_020177375.1_ASM2017737v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:02,086] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:02,089] [INFO] Selected 11 target genomes.
[2024-01-24 14:07:02,089] [INFO] Target genome list was writen to GCF_020177375.1_ASM2017737v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:02,097] [INFO] Task started: fastANI
[2024-01-24 14:07:02,097] [INFO] Running command: fastANI --query /var/lib/cwl/stga7a267f3-8828-4637-80f9-dd1b95cf0b6c/GCF_020177375.1_ASM2017737v1_genomic.fna.gz --refList GCF_020177375.1_ASM2017737v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020177375.1_ASM2017737v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:14,315] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:14,327] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:14,328] [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_003344565.1	s__Saliphagus sp003344565	97.0386	1168	1470	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Saliphagus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000337695.1	s__Natronococcus jeotgali	80.019	591	1470	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	95.54	95.54	0.86	0.86	2	-
GCF_017357405.1	s__KZCA124 sp017357405	79.3238	624	1470	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__KZCA124	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337675.1	s__Natronococcus amylolyticus	79.2945	550	1470	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352155.1	s__Haloterrigena sp017352155	79.2196	518	1470	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003559215.1	s__Natronococcus sp003559215	79.0515	508	1470	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	99.83	99.81	0.98	0.98	4	-
GCF_003610195.1	s__Halopiger aswanensis	78.9892	597	1470	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337495.1	s__Haloterrigena salina	78.9884	568	1470	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013342135.1	s__Haloterrigena sp013342135	78.8649	619	1470	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	99.13	99.13	0.91	0.91	2	-
GCF_008122205.1	s__Natronococcus sp008122205	78.8332	546	1470	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002494345.1	s__Natrinema ejinorense	78.7083	472	1470	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	95.42	95.42	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:14,329] [INFO] GTDB search result was written to GCF_020177375.1_ASM2017737v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:14,330] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:14,333] [INFO] DFAST_QC result json was written to GCF_020177375.1_ASM2017737v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:14,333] [INFO] DFAST_QC completed!
[2024-01-24 14:07:14,333] [INFO] Total running time: 0h1m43s