[2023-06-16 22:51:50,016] [INFO] DFAST_QC pipeline started.
[2023-06-16 22:51:50,020] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 22:51:50,020] [INFO] DQC Reference Directory: /var/lib/cwl/stgdcdb3bcb-cb88-4dec-b26f-0da38f6f6a3b/dqc_reference
[2023-06-16 22:51:52,283] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 22:51:52,284] [INFO] Task started: Prodigal
[2023-06-16 22:51:52,285] [INFO] Running command: gunzip -c /var/lib/cwl/stg9bafbae6-5b17-4c04-9128-f46b8be52968/GCA_009835535.1_ASM983553v1_genomic.fna.gz | prodigal -d GCA_009835535.1_ASM983553v1_genomic.fna/cds.fna -a GCA_009835535.1_ASM983553v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 22:52:03,452] [INFO] Task succeeded: Prodigal
[2023-06-16 22:52:03,452] [INFO] Task started: HMMsearch
[2023-06-16 22:52:03,453] [INFO] Running command: hmmsearch --tblout GCA_009835535.1_ASM983553v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdcdb3bcb-cb88-4dec-b26f-0da38f6f6a3b/dqc_reference/reference_markers.hmm GCA_009835535.1_ASM983553v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 22:52:03,779] [INFO] Task succeeded: HMMsearch
[2023-06-16 22:52:03,781] [INFO] Found 6/6 markers.
[2023-06-16 22:52:03,822] [INFO] Query marker FASTA was written to GCA_009835535.1_ASM983553v1_genomic.fna/markers.fasta
[2023-06-16 22:52:03,822] [INFO] Task started: Blastn
[2023-06-16 22:52:03,822] [INFO] Running command: blastn -query GCA_009835535.1_ASM983553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcdb3bcb-cb88-4dec-b26f-0da38f6f6a3b/dqc_reference/reference_markers.fasta -out GCA_009835535.1_ASM983553v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:52:04,505] [INFO] Task succeeded: Blastn
[2023-06-16 22:52:04,510] [INFO] Selected 25 target genomes.
[2023-06-16 22:52:04,511] [INFO] Target genome list was writen to GCA_009835535.1_ASM983553v1_genomic.fna/target_genomes.txt
[2023-06-16 22:52:04,520] [INFO] Task started: fastANI
[2023-06-16 22:52:04,520] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bafbae6-5b17-4c04-9128-f46b8be52968/GCA_009835535.1_ASM983553v1_genomic.fna.gz --refList GCA_009835535.1_ASM983553v1_genomic.fna/target_genomes.txt --output GCA_009835535.1_ASM983553v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 22:52:26,990] [INFO] Task succeeded: fastANI
[2023-06-16 22:52:26,991] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdcdb3bcb-cb88-4dec-b26f-0da38f6f6a3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 22:52:26,991] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdcdb3bcb-cb88-4dec-b26f-0da38f6f6a3b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 22:52:27,014] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 22:52:27,015] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 22:52:27,015] [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
Luteitalea pratensis	strain=DSM 100886; HEG_-6_39	GCA_001618865.1	1855912	1855912	type	True	75.4558	93	1471	95	below_threshold
Pelagibius marinus	strain=NBU2595	GCA_014925385.1	2762760	2762760	type	True	75.2455	92	1471	95	below_threshold
Microvirga subterranea	strain=DSM 14364	GCA_003350535.1	186651	186651	type	True	75.1817	62	1471	95	below_threshold
Plasticicumulans lactativorans	strain=DSM 25287	GCA_004341245.1	1133106	1133106	type	True	75.1282	118	1471	95	below_threshold
Malikia granosa	strain=P1	GCA_002980595.1	263067	263067	type	True	75.0889	77	1471	95	below_threshold
Motilibacter aurantiacus	strain=K478	GCA_011250645.1	2714955	2714955	type	True	74.9948	107	1471	95	below_threshold
Salsipaludibacter albus	strain=AS10	GCA_019798055.1	2849650	2849650	type	True	74.9414	79	1471	95	below_threshold
Pyxidicoccus caerfyrddinensis	strain=CA032A	GCA_010894405.1	2709663	2709663	type	True	74.9015	134	1471	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	74.901	219	1471	95	below_threshold
Azospirillum oleiclasticum	strain=RWY-5-1-1	GCA_013423485.1	2735135	2735135	type	True	74.8879	143	1471	95	below_threshold
Actinomadura atramentaria	strain=SF2197	GCA_000381885.1	1990	1990	type	True	74.8831	149	1471	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	74.8763	98	1471	95	below_threshold
Pyxidicoccus trucidator	strain=CA060A	GCA_010894435.1	2709662	2709662	type	True	74.8461	107	1471	95	below_threshold
Frankia asymbiotica	strain=NRRL B-16386	GCA_001983105.1	1834516	1834516	type	True	74.8182	189	1471	95	below_threshold
Methylobacterium nonmethylotrophicum	strain=6HR-1	GCA_004745635.1	1141884	1141884	type	True	74.8067	179	1471	95	below_threshold
Pseudomonas jinjuensis	strain=JCM 21621	GCA_900103845.1	198616	198616	type	True	74.7971	84	1471	95	below_threshold
Paraconexibacter algicola	strain=Seoho-28	GCA_003044185.1	2133960	2133960	type	True	74.7633	134	1471	95	below_threshold
Archangium violaceum	strain=Cb vi76	GCA_000733295.1	83451	83451	type	True	74.7444	113	1471	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 22:52:27,017] [INFO] DFAST Taxonomy check result was written to GCA_009835535.1_ASM983553v1_genomic.fna/tc_result.tsv
[2023-06-16 22:52:27,018] [INFO] ===== Taxonomy check completed =====
[2023-06-16 22:52:27,018] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 22:52:27,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdcdb3bcb-cb88-4dec-b26f-0da38f6f6a3b/dqc_reference/checkm_data
[2023-06-16 22:52:27,020] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 22:52:27,069] [INFO] Task started: CheckM
[2023-06-16 22:52:27,070] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009835535.1_ASM983553v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009835535.1_ASM983553v1_genomic.fna/checkm_input GCA_009835535.1_ASM983553v1_genomic.fna/checkm_result
[2023-06-16 22:53:02,642] [INFO] Task succeeded: CheckM
[2023-06-16 22:53:02,644] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 22:53:02,666] [INFO] ===== Completeness check finished =====
[2023-06-16 22:53:02,666] [INFO] ===== Start GTDB Search =====
[2023-06-16 22:53:02,667] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009835535.1_ASM983553v1_genomic.fna/markers.fasta)
[2023-06-16 22:53:02,667] [INFO] Task started: Blastn
[2023-06-16 22:53:02,667] [INFO] Running command: blastn -query GCA_009835535.1_ASM983553v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdcdb3bcb-cb88-4dec-b26f-0da38f6f6a3b/dqc_reference/reference_markers_gtdb.fasta -out GCA_009835535.1_ASM983553v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 22:53:03,622] [INFO] Task succeeded: Blastn
[2023-06-16 22:53:03,627] [INFO] Selected 7 target genomes.
[2023-06-16 22:53:03,627] [INFO] Target genome list was writen to GCA_009835535.1_ASM983553v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 22:53:03,637] [INFO] Task started: fastANI
[2023-06-16 22:53:03,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg9bafbae6-5b17-4c04-9128-f46b8be52968/GCA_009835535.1_ASM983553v1_genomic.fna.gz --refList GCA_009835535.1_ASM983553v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009835535.1_ASM983553v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 22:53:12,121] [INFO] Task succeeded: fastANI
[2023-06-16 22:53:12,130] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-16 22:53:12,130] [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_009836625.1	s__WTGL01 sp009836625	98.0937	1307	1471	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.03	98.03	0.95	0.91	5	conclusive
GCA_009845425.1	s__WTGL01 sp009845425	94.7627	1280	1471	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.99	99.99	0.99	0.99	3	-
GCA_009837885.1	s__WTGL01 sp009837885	92.8743	1249	1471	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.92	99.92	0.99	0.99	2	-
GCA_009843505.1	s__WTGL01 sp009843505	92.3839	1249	1471	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.97	99.97	0.99	0.99	2	-
GCA_011525365.1	s__WTGL01 sp011525365	92.175	1237	1471	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009837085.1	s__WTGL01 sp009837085	91.8155	1160	1471	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	99.78	99.78	0.96	0.95	3	-
GCA_012270995.1	s__WTGL01 sp012270995	87.5424	1096	1471	d__Bacteria;p__Acidobacteriota;c__Thermoanaerobaculia;o__UBA5704;f__QQVD01;g__WTGL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 22:53:12,132] [INFO] GTDB search result was written to GCA_009835535.1_ASM983553v1_genomic.fna/result_gtdb.tsv
[2023-06-16 22:53:12,133] [INFO] ===== GTDB Search completed =====
[2023-06-16 22:53:12,137] [INFO] DFAST_QC result json was written to GCA_009835535.1_ASM983553v1_genomic.fna/dqc_result.json
[2023-06-16 22:53:12,137] [INFO] DFAST_QC completed!
[2023-06-16 22:53:12,137] [INFO] Total running time: 0h1m22s