[2023-06-28 12:18:15,936] [INFO] DFAST_QC pipeline started.
[2023-06-28 12:18:15,939] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 12:18:15,939] [INFO] DQC Reference Directory: /var/lib/cwl/stg5fc90958-cdbd-4519-b695-a71467614e22/dqc_reference
[2023-06-28 12:18:17,141] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 12:18:17,141] [INFO] Task started: Prodigal
[2023-06-28 12:18:17,142] [INFO] Running command: gunzip -c /var/lib/cwl/stg43347441-a5be-40b6-8609-0492bc9cfcf2/GCA_017384015.1_ASM1738401v1_genomic.fna.gz | prodigal -d GCA_017384015.1_ASM1738401v1_genomic.fna/cds.fna -a GCA_017384015.1_ASM1738401v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 12:18:23,556] [INFO] Task succeeded: Prodigal
[2023-06-28 12:18:23,557] [INFO] Task started: HMMsearch
[2023-06-28 12:18:23,557] [INFO] Running command: hmmsearch --tblout GCA_017384015.1_ASM1738401v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5fc90958-cdbd-4519-b695-a71467614e22/dqc_reference/reference_markers.hmm GCA_017384015.1_ASM1738401v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 12:18:23,760] [INFO] Task succeeded: HMMsearch
[2023-06-28 12:18:23,761] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg43347441-a5be-40b6-8609-0492bc9cfcf2/GCA_017384015.1_ASM1738401v1_genomic.fna.gz]
[2023-06-28 12:18:23,784] [INFO] Query marker FASTA was written to GCA_017384015.1_ASM1738401v1_genomic.fna/markers.fasta
[2023-06-28 12:18:23,784] [INFO] Task started: Blastn
[2023-06-28 12:18:23,784] [INFO] Running command: blastn -query GCA_017384015.1_ASM1738401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fc90958-cdbd-4519-b695-a71467614e22/dqc_reference/reference_markers.fasta -out GCA_017384015.1_ASM1738401v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:18:24,404] [INFO] Task succeeded: Blastn
[2023-06-28 12:18:24,409] [INFO] Selected 25 target genomes.
[2023-06-28 12:18:24,410] [INFO] Target genome list was writen to GCA_017384015.1_ASM1738401v1_genomic.fna/target_genomes.txt
[2023-06-28 12:18:24,414] [INFO] Task started: fastANI
[2023-06-28 12:18:24,414] [INFO] Running command: fastANI --query /var/lib/cwl/stg43347441-a5be-40b6-8609-0492bc9cfcf2/GCA_017384015.1_ASM1738401v1_genomic.fna.gz --refList GCA_017384015.1_ASM1738401v1_genomic.fna/target_genomes.txt --output GCA_017384015.1_ASM1738401v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 12:18:38,316] [INFO] Task succeeded: fastANI
[2023-06-28 12:18:38,317] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5fc90958-cdbd-4519-b695-a71467614e22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 12:18:38,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5fc90958-cdbd-4519-b695-a71467614e22/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 12:18:38,318] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 12:18:38,319] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-28 12:18:38,319] [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
--------------------------------------------------------------------------------
[2023-06-28 12:18:38,321] [INFO] DFAST Taxonomy check result was written to GCA_017384015.1_ASM1738401v1_genomic.fna/tc_result.tsv
[2023-06-28 12:18:38,321] [INFO] ===== Taxonomy check completed =====
[2023-06-28 12:18:38,321] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 12:18:38,322] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5fc90958-cdbd-4519-b695-a71467614e22/dqc_reference/checkm_data
[2023-06-28 12:18:38,326] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 12:18:38,345] [INFO] Task started: CheckM
[2023-06-28 12:18:38,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_017384015.1_ASM1738401v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_017384015.1_ASM1738401v1_genomic.fna/checkm_input GCA_017384015.1_ASM1738401v1_genomic.fna/checkm_result
[2023-06-28 12:19:02,776] [INFO] Task succeeded: CheckM
[2023-06-28 12:19:02,777] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 27.08%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-28 12:19:02,802] [INFO] ===== Completeness check finished =====
[2023-06-28 12:19:02,802] [INFO] ===== Start GTDB Search =====
[2023-06-28 12:19:02,803] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_017384015.1_ASM1738401v1_genomic.fna/markers.fasta)
[2023-06-28 12:19:02,803] [INFO] Task started: Blastn
[2023-06-28 12:19:02,803] [INFO] Running command: blastn -query GCA_017384015.1_ASM1738401v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5fc90958-cdbd-4519-b695-a71467614e22/dqc_reference/reference_markers_gtdb.fasta -out GCA_017384015.1_ASM1738401v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 12:19:03,782] [INFO] Task succeeded: Blastn
[2023-06-28 12:19:03,787] [INFO] Selected 13 target genomes.
[2023-06-28 12:19:03,788] [INFO] Target genome list was writen to GCA_017384015.1_ASM1738401v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 12:19:03,793] [INFO] Task started: fastANI
[2023-06-28 12:19:03,793] [INFO] Running command: fastANI --query /var/lib/cwl/stg43347441-a5be-40b6-8609-0492bc9cfcf2/GCA_017384015.1_ASM1738401v1_genomic.fna.gz --refList GCA_017384015.1_ASM1738401v1_genomic.fna/target_genomes_gtdb.txt --output GCA_017384015.1_ASM1738401v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 12:19:08,057] [INFO] Task succeeded: fastANI
[2023-06-28 12:19:08,076] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 12:19:08,077] [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_017474235.1	s__Alistipes sp017474235	97.7493	293	301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.76	97.70	0.93	0.92	3	conclusive
GCA_017398555.1	s__Alistipes sp017398555	80.7169	236	301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.22	97.01	0.91	0.90	4	-
GCA_017938765.1	s__Alistipes sp017938765	79.8275	196	301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.68	97.68	0.94	0.94	2	-
GCA_015059805.1	s__Alistipes sp015059805	79.5217	191	301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.01	97.01	0.81	0.81	2	-
GCA_015059785.1	s__Alistipes sp015059785	79.4695	195	301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	97.23	97.23	0.91	0.91	2	-
GCA_017463615.1	s__Alistipes sp017463615	79.2697	204	301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_904502005.1	s__Alistipes sp904502005	79.0222	149	301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	100.00	100.00	0.99	0.99	2	-
GCA_017391435.1	s__Alistipes sp017391435	78.9109	118	301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017381935.1	s__Alistipes sp017381935	78.7987	157	301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017507075.1	s__Alistipes sp017507075	78.5883	150	301	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Rikenellaceae;g__Alistipes	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 12:19:08,079] [INFO] GTDB search result was written to GCA_017384015.1_ASM1738401v1_genomic.fna/result_gtdb.tsv
[2023-06-28 12:19:08,080] [INFO] ===== GTDB Search completed =====
[2023-06-28 12:19:08,083] [INFO] DFAST_QC result json was written to GCA_017384015.1_ASM1738401v1_genomic.fna/dqc_result.json
[2023-06-28 12:19:08,083] [INFO] DFAST_QC completed!
[2023-06-28 12:19:08,083] [INFO] Total running time: 0h0m52s