[2023-06-18 20:56:23,931] [INFO] DFAST_QC pipeline started.
[2023-06-18 20:56:23,935] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 20:56:23,936] [INFO] DQC Reference Directory: /var/lib/cwl/stgede99ab3-e479-4aa7-a51c-c02c012b35a6/dqc_reference
[2023-06-18 20:56:25,210] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 20:56:25,211] [INFO] Task started: Prodigal
[2023-06-18 20:56:25,211] [INFO] Running command: gunzip -c /var/lib/cwl/stg87e7df81-e447-426c-863b-c4d9c6a0ec55/GCA_018054045.1_ASM1805404v1_genomic.fna.gz | prodigal -d GCA_018054045.1_ASM1805404v1_genomic.fna/cds.fna -a GCA_018054045.1_ASM1805404v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 20:56:30,064] [INFO] Task succeeded: Prodigal
[2023-06-18 20:56:30,065] [INFO] Task started: HMMsearch
[2023-06-18 20:56:30,065] [INFO] Running command: hmmsearch --tblout GCA_018054045.1_ASM1805404v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgede99ab3-e479-4aa7-a51c-c02c012b35a6/dqc_reference/reference_markers.hmm GCA_018054045.1_ASM1805404v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 20:56:30,304] [INFO] Task succeeded: HMMsearch
[2023-06-18 20:56:30,305] [INFO] Found 6/6 markers.
[2023-06-18 20:56:30,343] [INFO] Query marker FASTA was written to GCA_018054045.1_ASM1805404v1_genomic.fna/markers.fasta
[2023-06-18 20:56:30,344] [INFO] Task started: Blastn
[2023-06-18 20:56:30,344] [INFO] Running command: blastn -query GCA_018054045.1_ASM1805404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgede99ab3-e479-4aa7-a51c-c02c012b35a6/dqc_reference/reference_markers.fasta -out GCA_018054045.1_ASM1805404v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:56:30,941] [INFO] Task succeeded: Blastn
[2023-06-18 20:56:30,946] [INFO] Selected 22 target genomes.
[2023-06-18 20:56:30,947] [INFO] Target genome list was writen to GCA_018054045.1_ASM1805404v1_genomic.fna/target_genomes.txt
[2023-06-18 20:56:30,952] [INFO] Task started: fastANI
[2023-06-18 20:56:30,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg87e7df81-e447-426c-863b-c4d9c6a0ec55/GCA_018054045.1_ASM1805404v1_genomic.fna.gz --refList GCA_018054045.1_ASM1805404v1_genomic.fna/target_genomes.txt --output GCA_018054045.1_ASM1805404v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 20:56:42,272] [INFO] Task succeeded: fastANI
[2023-06-18 20:56:42,273] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgede99ab3-e479-4aa7-a51c-c02c012b35a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 20:56:42,274] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgede99ab3-e479-4aa7-a51c-c02c012b35a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 20:56:42,283] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2023-06-18 20:56:42,283] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-18 20:56:42,283] [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
Wujia chipingensis	strain=NSJ-4	GCA_014337155.1	2763670	2763670	type	True	98.8575	554	574	95	conclusive
Coprococcus eutactus	strain=ATCC 27759	GCA_000154425.1	33043	33043	suspected-type	True	78.5576	62	574	95	below_threshold
Coprococcus eutactus	strain=ATCC 27759	GCA_025149915.1	33043	33043	suspected-type	True	78.5534	62	574	95	below_threshold
Jutongia huaianensis	strain=NSJ-37	GCA_014384985.1	2763668	2763668	type	True	76.5466	54	574	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 20:56:42,285] [INFO] DFAST Taxonomy check result was written to GCA_018054045.1_ASM1805404v1_genomic.fna/tc_result.tsv
[2023-06-18 20:56:42,286] [INFO] ===== Taxonomy check completed =====
[2023-06-18 20:56:42,286] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 20:56:42,286] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgede99ab3-e479-4aa7-a51c-c02c012b35a6/dqc_reference/checkm_data
[2023-06-18 20:56:42,288] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 20:56:42,310] [INFO] Task started: CheckM
[2023-06-18 20:56:42,311] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018054045.1_ASM1805404v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018054045.1_ASM1805404v1_genomic.fna/checkm_input GCA_018054045.1_ASM1805404v1_genomic.fna/checkm_result
[2023-06-18 20:57:04,266] [INFO] Task succeeded: CheckM
[2023-06-18 20:57:04,267] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 20:57:04,285] [INFO] ===== Completeness check finished =====
[2023-06-18 20:57:04,285] [INFO] ===== Start GTDB Search =====
[2023-06-18 20:57:04,286] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018054045.1_ASM1805404v1_genomic.fna/markers.fasta)
[2023-06-18 20:57:04,286] [INFO] Task started: Blastn
[2023-06-18 20:57:04,287] [INFO] Running command: blastn -query GCA_018054045.1_ASM1805404v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgede99ab3-e479-4aa7-a51c-c02c012b35a6/dqc_reference/reference_markers_gtdb.fasta -out GCA_018054045.1_ASM1805404v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 20:57:05,118] [INFO] Task succeeded: Blastn
[2023-06-18 20:57:05,122] [INFO] Selected 7 target genomes.
[2023-06-18 20:57:05,122] [INFO] Target genome list was writen to GCA_018054045.1_ASM1805404v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 20:57:05,129] [INFO] Task started: fastANI
[2023-06-18 20:57:05,129] [INFO] Running command: fastANI --query /var/lib/cwl/stg87e7df81-e447-426c-863b-c4d9c6a0ec55/GCA_018054045.1_ASM1805404v1_genomic.fna.gz --refList GCA_018054045.1_ASM1805404v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018054045.1_ASM1805404v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 20:57:09,130] [INFO] Task succeeded: fastANI
[2023-06-18 20:57:09,147] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 20:57:09,147] [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_014337155.1	s__CAG-127 sp900319515	98.8575	554	574	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	98.02	96.09	0.90	0.85	25	conclusive
GCA_002431865.1	s__CAG-127 sp002431865	91.9924	460	574	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	99.73	99.73	0.84	0.84	3	-
GCA_002404515.1	s__CAG-127 sp002404515	90.7834	426	574	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018918185.1	s__CAG-127 sp900539705	90.6887	520	574	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	97.05	96.96	0.87	0.83	4	-
GCA_900553925.1	s__CAG-127 sp900553925	88.9837	351	574	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	97.14	96.66	0.89	0.85	4	-
GCA_900767585.1	s__CAG-127 sp900767585	88.0476	414	574	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017938485.1	s__CAG-127 sp017938485	77.6999	74	574	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-127	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 20:57:09,150] [INFO] GTDB search result was written to GCA_018054045.1_ASM1805404v1_genomic.fna/result_gtdb.tsv
[2023-06-18 20:57:09,151] [INFO] ===== GTDB Search completed =====
[2023-06-18 20:57:09,157] [INFO] DFAST_QC result json was written to GCA_018054045.1_ASM1805404v1_genomic.fna/dqc_result.json
[2023-06-18 20:57:09,158] [INFO] DFAST_QC completed!
[2023-06-18 20:57:09,158] [INFO] Total running time: 0h0m45s