[2023-06-29 12:38:09,856] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:38:09,859] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:38:09,859] [INFO] DQC Reference Directory: /var/lib/cwl/stg70a0dbd2-df41-41f1-b8da-75003ec76843/dqc_reference
[2023-06-29 12:38:11,046] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:38:11,047] [INFO] Task started: Prodigal
[2023-06-29 12:38:11,047] [INFO] Running command: gunzip -c /var/lib/cwl/stg0428ccf3-1128-4c76-879f-46fccf77ddd0/GCA_021626285.1_ASM2162628v1_genomic.fna.gz | prodigal -d GCA_021626285.1_ASM2162628v1_genomic.fna/cds.fna -a GCA_021626285.1_ASM2162628v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:38:15,785] [INFO] Task succeeded: Prodigal
[2023-06-29 12:38:15,786] [INFO] Task started: HMMsearch
[2023-06-29 12:38:15,786] [INFO] Running command: hmmsearch --tblout GCA_021626285.1_ASM2162628v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg70a0dbd2-df41-41f1-b8da-75003ec76843/dqc_reference/reference_markers.hmm GCA_021626285.1_ASM2162628v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:38:15,995] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:38:15,996] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0428ccf3-1128-4c76-879f-46fccf77ddd0/GCA_021626285.1_ASM2162628v1_genomic.fna.gz]
[2023-06-29 12:38:16,016] [INFO] Query marker FASTA was written to GCA_021626285.1_ASM2162628v1_genomic.fna/markers.fasta
[2023-06-29 12:38:16,016] [INFO] Task started: Blastn
[2023-06-29 12:38:16,017] [INFO] Running command: blastn -query GCA_021626285.1_ASM2162628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70a0dbd2-df41-41f1-b8da-75003ec76843/dqc_reference/reference_markers.fasta -out GCA_021626285.1_ASM2162628v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:38:16,621] [INFO] Task succeeded: Blastn
[2023-06-29 12:38:16,625] [INFO] Selected 16 target genomes.
[2023-06-29 12:38:16,626] [INFO] Target genome list was writen to GCA_021626285.1_ASM2162628v1_genomic.fna/target_genomes.txt
[2023-06-29 12:38:16,629] [INFO] Task started: fastANI
[2023-06-29 12:38:16,629] [INFO] Running command: fastANI --query /var/lib/cwl/stg0428ccf3-1128-4c76-879f-46fccf77ddd0/GCA_021626285.1_ASM2162628v1_genomic.fna.gz --refList GCA_021626285.1_ASM2162628v1_genomic.fna/target_genomes.txt --output GCA_021626285.1_ASM2162628v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:38:26,126] [INFO] Task succeeded: fastANI
[2023-06-29 12:38:26,127] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg70a0dbd2-df41-41f1-b8da-75003ec76843/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:38:26,127] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg70a0dbd2-df41-41f1-b8da-75003ec76843/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:38:26,132] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:38:26,132] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 12:38:26,132] [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
--------------------------------------------------------------------------------
[2023-06-29 12:38:26,136] [INFO] DFAST Taxonomy check result was written to GCA_021626285.1_ASM2162628v1_genomic.fna/tc_result.tsv
[2023-06-29 12:38:26,136] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:38:26,137] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:38:26,137] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg70a0dbd2-df41-41f1-b8da-75003ec76843/dqc_reference/checkm_data
[2023-06-29 12:38:26,142] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:38:26,168] [INFO] Task started: CheckM
[2023-06-29 12:38:26,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021626285.1_ASM2162628v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021626285.1_ASM2162628v1_genomic.fna/checkm_input GCA_021626285.1_ASM2162628v1_genomic.fna/checkm_result
[2023-06-29 12:38:47,186] [INFO] Task succeeded: CheckM
[2023-06-29 12:38:47,188] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.38%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-29 12:38:47,212] [INFO] ===== Completeness check finished =====
[2023-06-29 12:38:47,212] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:38:47,213] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021626285.1_ASM2162628v1_genomic.fna/markers.fasta)
[2023-06-29 12:38:47,213] [INFO] Task started: Blastn
[2023-06-29 12:38:47,214] [INFO] Running command: blastn -query GCA_021626285.1_ASM2162628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg70a0dbd2-df41-41f1-b8da-75003ec76843/dqc_reference/reference_markers_gtdb.fasta -out GCA_021626285.1_ASM2162628v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:38:48,193] [INFO] Task succeeded: Blastn
[2023-06-29 12:38:48,197] [INFO] Selected 10 target genomes.
[2023-06-29 12:38:48,198] [INFO] Target genome list was writen to GCA_021626285.1_ASM2162628v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:38:48,204] [INFO] Task started: fastANI
[2023-06-29 12:38:48,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg0428ccf3-1128-4c76-879f-46fccf77ddd0/GCA_021626285.1_ASM2162628v1_genomic.fna.gz --refList GCA_021626285.1_ASM2162628v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021626285.1_ASM2162628v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:38:51,798] [INFO] Task succeeded: fastANI
[2023-06-29 12:38:51,811] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:38:51,811] [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_000432015.1	s__CAG-1024 sp000432015	98.8448	444	525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__CAG-1024	95.0	98.73	98.71	0.87	0.85	5	conclusive
GCA_004554165.1	s__CAG-1024 sp004554165	79.3051	181	525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__CAG-1024	95.0	98.83	98.73	0.93	0.90	3	-
GCA_900550525.1	s__Aphodomorpha intestinavium	78.6411	98	525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__Aphodomorpha	95.0	98.57	98.50	0.86	0.85	3	-
GCA_900549955.1	s__Aphodomorpha sp900549955	78.3719	94	525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__Aphodomorpha	95.0	100.00	100.00	0.93	0.93	2	-
GCA_900540495.1	s__Aphodomorpha sp900540495	78.3549	104	525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__Aphodomorpha	95.0	99.44	99.00	0.94	0.92	3	-
GCA_012517905.1	s__UBA7703 sp012517905	77.6805	83	525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__UBA7703	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017429985.1	s__CAG-1024 sp017429985	77.4697	60	525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__CAG-1024	95.0	98.78	98.78	0.87	0.87	2	-
GCA_016286445.1	s__UBA3792 sp016286445	77.1595	60	525	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__UBA3792	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 12:38:51,813] [INFO] GTDB search result was written to GCA_021626285.1_ASM2162628v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:38:51,814] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:38:51,816] [INFO] DFAST_QC result json was written to GCA_021626285.1_ASM2162628v1_genomic.fna/dqc_result.json
[2023-06-29 12:38:51,816] [INFO] DFAST_QC completed!
[2023-06-29 12:38:51,817] [INFO] Total running time: 0h0m42s