[2023-06-17 09:32:10,602] [INFO] DFAST_QC pipeline started.
[2023-06-17 09:32:10,605] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 09:32:10,605] [INFO] DQC Reference Directory: /var/lib/cwl/stgb5d61a39-2afa-4f42-9be1-54538a3f8044/dqc_reference
[2023-06-17 09:32:13,269] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 09:32:13,269] [INFO] Task started: Prodigal
[2023-06-17 09:32:13,270] [INFO] Running command: gunzip -c /var/lib/cwl/stg6e122cf0-2fd4-4e34-94c2-8cf88a3c0f62/GCA_028704385.1_ASM2870438v1_genomic.fna.gz | prodigal -d GCA_028704385.1_ASM2870438v1_genomic.fna/cds.fna -a GCA_028704385.1_ASM2870438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 09:32:29,746] [INFO] Task succeeded: Prodigal
[2023-06-17 09:32:29,746] [INFO] Task started: HMMsearch
[2023-06-17 09:32:29,746] [INFO] Running command: hmmsearch --tblout GCA_028704385.1_ASM2870438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb5d61a39-2afa-4f42-9be1-54538a3f8044/dqc_reference/reference_markers.hmm GCA_028704385.1_ASM2870438v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 09:32:30,061] [INFO] Task succeeded: HMMsearch
[2023-06-17 09:32:30,062] [INFO] Found 6/6 markers.
[2023-06-17 09:32:30,126] [INFO] Query marker FASTA was written to GCA_028704385.1_ASM2870438v1_genomic.fna/markers.fasta
[2023-06-17 09:32:30,126] [INFO] Task started: Blastn
[2023-06-17 09:32:30,126] [INFO] Running command: blastn -query GCA_028704385.1_ASM2870438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5d61a39-2afa-4f42-9be1-54538a3f8044/dqc_reference/reference_markers.fasta -out GCA_028704385.1_ASM2870438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:32:30,854] [INFO] Task succeeded: Blastn
[2023-06-17 09:32:30,858] [INFO] Selected 34 target genomes.
[2023-06-17 09:32:30,859] [INFO] Target genome list was writen to GCA_028704385.1_ASM2870438v1_genomic.fna/target_genomes.txt
[2023-06-17 09:32:30,885] [INFO] Task started: fastANI
[2023-06-17 09:32:30,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e122cf0-2fd4-4e34-94c2-8cf88a3c0f62/GCA_028704385.1_ASM2870438v1_genomic.fna.gz --refList GCA_028704385.1_ASM2870438v1_genomic.fna/target_genomes.txt --output GCA_028704385.1_ASM2870438v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 09:32:55,541] [INFO] Task succeeded: fastANI
[2023-06-17 09:32:55,542] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb5d61a39-2afa-4f42-9be1-54538a3f8044/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 09:32:55,542] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb5d61a39-2afa-4f42-9be1-54538a3f8044/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 09:32:55,549] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 09:32:55,550] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-17 09:32:55,551] [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
--------------------------------------------------------------------------------
[2023-06-17 09:32:55,553] [INFO] DFAST Taxonomy check result was written to GCA_028704385.1_ASM2870438v1_genomic.fna/tc_result.tsv
[2023-06-17 09:32:55,554] [INFO] ===== Taxonomy check completed =====
[2023-06-17 09:32:55,554] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 09:32:55,555] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb5d61a39-2afa-4f42-9be1-54538a3f8044/dqc_reference/checkm_data
[2023-06-17 09:32:55,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 09:32:55,621] [INFO] Task started: CheckM
[2023-06-17 09:32:55,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028704385.1_ASM2870438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028704385.1_ASM2870438v1_genomic.fna/checkm_input GCA_028704385.1_ASM2870438v1_genomic.fna/checkm_result
[2023-06-17 09:33:46,880] [INFO] Task succeeded: CheckM
[2023-06-17 09:33:46,882] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 09:33:46,902] [INFO] ===== Completeness check finished =====
[2023-06-17 09:33:46,902] [INFO] ===== Start GTDB Search =====
[2023-06-17 09:33:46,903] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028704385.1_ASM2870438v1_genomic.fna/markers.fasta)
[2023-06-17 09:33:46,903] [INFO] Task started: Blastn
[2023-06-17 09:33:46,904] [INFO] Running command: blastn -query GCA_028704385.1_ASM2870438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb5d61a39-2afa-4f42-9be1-54538a3f8044/dqc_reference/reference_markers_gtdb.fasta -out GCA_028704385.1_ASM2870438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 09:33:48,078] [INFO] Task succeeded: Blastn
[2023-06-17 09:33:48,083] [INFO] Selected 22 target genomes.
[2023-06-17 09:33:48,083] [INFO] Target genome list was writen to GCA_028704385.1_ASM2870438v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 09:33:48,101] [INFO] Task started: fastANI
[2023-06-17 09:33:48,101] [INFO] Running command: fastANI --query /var/lib/cwl/stg6e122cf0-2fd4-4e34-94c2-8cf88a3c0f62/GCA_028704385.1_ASM2870438v1_genomic.fna.gz --refList GCA_028704385.1_ASM2870438v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028704385.1_ASM2870438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 09:34:00,468] [INFO] Task succeeded: fastANI
[2023-06-17 09:34:00,485] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 09:34:00,485] [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_002440975.1	s__UBA5536 sp002440975	86.5147	830	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__UBA5536	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015709215.1	s__UBA5536 sp015709215	80.5797	602	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__UBA5536	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018399335.1	s__UBA5536 sp018399335	80.1688	360	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__UBA5536	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018830105.1	s__UBA5536 sp018830105	78.0491	291	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__UBA5536	95.0	99.92	99.91	0.94	0.94	3	-
GCA_002426795.1	s__UBA5536 sp002426795	76.7755	145	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__UBA5536	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018400955.1	s__UBA6192 sp018400955	76.4658	84	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__UBA6192	95.0	98.67	98.67	0.78	0.78	2	-
GCA_018336075.1	s__UBA6192 sp018336075	76.1662	68	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__UBA6192	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009773165.1	s__UBA6192 sp009773165	75.9381	66	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__UBA6192	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002422725.1	s__UBA6192 sp002422725	75.8357	71	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__UBA6192	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013141455.1	s__UBA6192 sp013141455	75.6715	72	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__UBA6192	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903891085.1	s__UBA6192 sp903891085	75.6403	75	1120	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__UBA6192	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 09:34:00,487] [INFO] GTDB search result was written to GCA_028704385.1_ASM2870438v1_genomic.fna/result_gtdb.tsv
[2023-06-17 09:34:00,488] [INFO] ===== GTDB Search completed =====
[2023-06-17 09:34:00,491] [INFO] DFAST_QC result json was written to GCA_028704385.1_ASM2870438v1_genomic.fna/dqc_result.json
[2023-06-17 09:34:00,491] [INFO] DFAST_QC completed!
[2023-06-17 09:34:00,492] [INFO] Total running time: 0h1m50s