[2023-06-27 18:06:34,456] [INFO] DFAST_QC pipeline started.
[2023-06-27 18:06:34,459] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 18:06:34,460] [INFO] DQC Reference Directory: /var/lib/cwl/stg64f0f7db-ca87-4922-bef3-b8b4e1a19a9d/dqc_reference
[2023-06-27 18:06:35,750] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 18:06:35,751] [INFO] Task started: Prodigal
[2023-06-27 18:06:35,751] [INFO] Running command: gunzip -c /var/lib/cwl/stg6de41176-e7eb-4d11-aa97-cf5da3a72c37/GCA_026984635.1_ASM2698463v1_genomic.fna.gz | prodigal -d GCA_026984635.1_ASM2698463v1_genomic.fna/cds.fna -a GCA_026984635.1_ASM2698463v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 18:06:47,145] [INFO] Task succeeded: Prodigal
[2023-06-27 18:06:47,145] [INFO] Task started: HMMsearch
[2023-06-27 18:06:47,145] [INFO] Running command: hmmsearch --tblout GCA_026984635.1_ASM2698463v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64f0f7db-ca87-4922-bef3-b8b4e1a19a9d/dqc_reference/reference_markers.hmm GCA_026984635.1_ASM2698463v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 18:06:47,497] [INFO] Task succeeded: HMMsearch
[2023-06-27 18:06:47,498] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg6de41176-e7eb-4d11-aa97-cf5da3a72c37/GCA_026984635.1_ASM2698463v1_genomic.fna.gz]
[2023-06-27 18:06:47,538] [INFO] Query marker FASTA was written to GCA_026984635.1_ASM2698463v1_genomic.fna/markers.fasta
[2023-06-27 18:06:47,538] [INFO] Task started: Blastn
[2023-06-27 18:06:47,539] [INFO] Running command: blastn -query GCA_026984635.1_ASM2698463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64f0f7db-ca87-4922-bef3-b8b4e1a19a9d/dqc_reference/reference_markers.fasta -out GCA_026984635.1_ASM2698463v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:06:48,165] [INFO] Task succeeded: Blastn
[2023-06-27 18:06:48,168] [INFO] Selected 22 target genomes.
[2023-06-27 18:06:48,169] [INFO] Target genome list was writen to GCA_026984635.1_ASM2698463v1_genomic.fna/target_genomes.txt
[2023-06-27 18:06:48,175] [INFO] Task started: fastANI
[2023-06-27 18:06:48,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg6de41176-e7eb-4d11-aa97-cf5da3a72c37/GCA_026984635.1_ASM2698463v1_genomic.fna.gz --refList GCA_026984635.1_ASM2698463v1_genomic.fna/target_genomes.txt --output GCA_026984635.1_ASM2698463v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 18:07:02,479] [INFO] Task succeeded: fastANI
[2023-06-27 18:07:02,479] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64f0f7db-ca87-4922-bef3-b8b4e1a19a9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 18:07:02,480] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64f0f7db-ca87-4922-bef3-b8b4e1a19a9d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 18:07:02,489] [INFO] Found 9 fastANI hits (0 hits with ANI > threshold)
[2023-06-27 18:07:02,489] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-27 18:07:02,489] [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
Litorilinea aerophila	strain=ATCC BAA-2444	GCA_006569185.2	1204385	1204385	type	True	78.3947	455	1161	95	below_threshold
Caldilinea aerophila	strain=DSM 14535	GCA_000281175.1	133453	133453	type	True	76.3898	102	1161	95	below_threshold
Thermus caliditerrae	strain=YIM 77925	GCA_021462525.1	1330700	1330700	type	True	75.8692	84	1161	95	below_threshold
Thermoflexus hugenholtzii	strain=JAD2	GCA_900187885.1	1495650	1495650	type	True	75.8074	115	1161	95	below_threshold
Thermus oshimai	strain=DSM 12092	GCA_000373145.1	56957	56957	type	True	75.742	108	1161	95	below_threshold
Thermus aquaticus	strain=YT-1	GCA_001280255.1	271	271	type	True	75.6545	101	1161	95	below_threshold
Desulfohalovibrio reitneri	strain=L21-Syr-AB	GCA_000711295.1	1307759	1307759	type	True	75.4032	77	1161	95	below_threshold
Deferrisoma camini	strain=S3R1	GCA_000526155.1	1035120	1035120	type	True	75.2684	96	1161	95	below_threshold
Aminomonas paucivorans	strain=DSM 12260	GCA_000165795.1	81412	81412	type	True	75.2057	78	1161	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 18:07:02,491] [INFO] DFAST Taxonomy check result was written to GCA_026984635.1_ASM2698463v1_genomic.fna/tc_result.tsv
[2023-06-27 18:07:02,492] [INFO] ===== Taxonomy check completed =====
[2023-06-27 18:07:02,492] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 18:07:02,492] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64f0f7db-ca87-4922-bef3-b8b4e1a19a9d/dqc_reference/checkm_data
[2023-06-27 18:07:02,494] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 18:07:02,546] [INFO] Task started: CheckM
[2023-06-27 18:07:02,546] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026984635.1_ASM2698463v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026984635.1_ASM2698463v1_genomic.fna/checkm_input GCA_026984635.1_ASM2698463v1_genomic.fna/checkm_result
[2023-06-27 18:07:39,307] [INFO] Task succeeded: CheckM
[2023-06-27 18:07:39,308] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 7.32%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-27 18:07:39,333] [INFO] ===== Completeness check finished =====
[2023-06-27 18:07:39,334] [INFO] ===== Start GTDB Search =====
[2023-06-27 18:07:39,334] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026984635.1_ASM2698463v1_genomic.fna/markers.fasta)
[2023-06-27 18:07:39,334] [INFO] Task started: Blastn
[2023-06-27 18:07:39,334] [INFO] Running command: blastn -query GCA_026984635.1_ASM2698463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64f0f7db-ca87-4922-bef3-b8b4e1a19a9d/dqc_reference/reference_markers_gtdb.fasta -out GCA_026984635.1_ASM2698463v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:07:40,163] [INFO] Task succeeded: Blastn
[2023-06-27 18:07:40,167] [INFO] Selected 20 target genomes.
[2023-06-27 18:07:40,168] [INFO] Target genome list was writen to GCA_026984635.1_ASM2698463v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 18:07:40,174] [INFO] Task started: fastANI
[2023-06-27 18:07:40,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg6de41176-e7eb-4d11-aa97-cf5da3a72c37/GCA_026984635.1_ASM2698463v1_genomic.fna.gz --refList GCA_026984635.1_ASM2698463v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026984635.1_ASM2698463v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 18:07:56,264] [INFO] Task succeeded: fastANI
[2023-06-27 18:07:56,285] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-27 18:07:56,285] [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_015494005.1	s__S144-5 sp015494005	89.6571	742	1161	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__S144-5	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006569185.1	s__Litorilinea aerophila	78.3954	455	1161	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Litorilinea	95.0	99.85	99.85	0.99	0.99	2	-
GCA_018003515.1	s__JAGNDO01 sp018003515	77.2932	301	1161	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__JAGNDO01	95.0	99.87	99.85	0.92	0.92	4	-
GCA_009840225.1	s__Bin5 sp009840225	76.5653	92	1161	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	97.63	95.35	0.89	0.84	3	-
GCA_009838625.1	s__Bin5 sp009838625	76.4359	83	1161	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Bin5	95.0	99.90	99.90	0.97	0.97	2	-
GCA_015484715.1	s__S140-20 sp015484715	76.4163	89	1161	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__S140-20;f__S140-20;g__S140-20	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000281175.1	s__Caldilinea aerophila	76.4071	101	1161	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	97.04	95.81	0.94	0.92	4	-
GCA_016710365.1	s__Caldilinea sp016710365	76.3994	98	1161	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016124945.1	s__RI-153 sp016124945	76.3629	146	1161	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__RI-153	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016199425.1	s__JACQGT01 sp016199425	76.3186	141	1161	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__JACQGT01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016713335.1	s__JADJPH01 sp016713335	76.3069	68	1161	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__JADJPH01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903879975.1	s__Caldilinea sp903879975	76.1206	71	1161	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	98.69	98.69	0.81	0.81	2	-
GCA_003577005.1	s__CFX5 sp003577005	75.8625	91	1161	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__CFX5	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879855.1	s__Caldilinea sp014879855	75.4409	86	1161	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Caldilineales;f__Caldilineaceae;g__Caldilinea	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009268125.1	s__SDU3-3 sp009268125	75.3587	89	1161	d__Bacteria;p__Chloroflexota;c__Chloroflexia;o__Chloroflexales;f__Roseiflexaceae;g__SDU3-3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016789175.1	s__UBA6663 sp016789175	75.136	53	1161	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__Anaerolineales;f__UBA6663;g__UBA6663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002329325.1	s__UBA1429 sp002329325	74.8808	64	1161	d__Bacteria;p__Chloroflexota;c__Anaerolineae;o__UBA1429;f__UBA1429;g__UBA1429	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-27 18:07:56,288] [INFO] GTDB search result was written to GCA_026984635.1_ASM2698463v1_genomic.fna/result_gtdb.tsv
[2023-06-27 18:07:56,288] [INFO] ===== GTDB Search completed =====
[2023-06-27 18:07:56,292] [INFO] DFAST_QC result json was written to GCA_026984635.1_ASM2698463v1_genomic.fna/dqc_result.json
[2023-06-27 18:07:56,292] [INFO] DFAST_QC completed!
[2023-06-27 18:07:56,292] [INFO] Total running time: 0h1m22s