[2023-03-16 09:49:19,915] [INFO] DFAST_QC pipeline started.
[2023-03-16 09:49:19,915] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 09:49:19,916] [INFO] DQC Reference Directory: /var/lib/cwl/stg930a004c-e1ae-421f-a062-b02f733b9a60/dqc_reference
[2023-03-16 09:49:21,007] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 09:49:21,007] [INFO] Task started: Prodigal
[2023-03-16 09:49:21,007] [INFO] Running command: cat /var/lib/cwl/stg8e3156e2-1362-4a28-aec2-1583ed1f2e7b/OceanDNA-b46536.fa | prodigal -d OceanDNA-b46536/cds.fna -a OceanDNA-b46536/protein.faa -g 11 -q > /dev/null
[2023-03-16 09:49:38,915] [INFO] Task succeeded: Prodigal
[2023-03-16 09:49:38,916] [INFO] Task started: HMMsearch
[2023-03-16 09:49:38,916] [INFO] Running command: hmmsearch --tblout OceanDNA-b46536/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg930a004c-e1ae-421f-a062-b02f733b9a60/dqc_reference/reference_markers.hmm OceanDNA-b46536/protein.faa > /dev/null
[2023-03-16 09:49:39,085] [INFO] Task succeeded: HMMsearch
[2023-03-16 09:49:39,086] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg8e3156e2-1362-4a28-aec2-1583ed1f2e7b/OceanDNA-b46536.fa]
[2023-03-16 09:49:39,106] [INFO] Query marker FASTA was written to OceanDNA-b46536/markers.fasta
[2023-03-16 09:49:39,107] [INFO] Task started: Blastn
[2023-03-16 09:49:39,107] [INFO] Running command: blastn -query OceanDNA-b46536/markers.fasta -db /var/lib/cwl/stg930a004c-e1ae-421f-a062-b02f733b9a60/dqc_reference/reference_markers.fasta -out OceanDNA-b46536/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:49:39,623] [INFO] Task succeeded: Blastn
[2023-03-16 09:49:39,625] [INFO] Selected 19 target genomes.
[2023-03-16 09:49:39,625] [INFO] Target genome list was writen to OceanDNA-b46536/target_genomes.txt
[2023-03-16 09:49:39,637] [INFO] Task started: fastANI
[2023-03-16 09:49:39,637] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e3156e2-1362-4a28-aec2-1583ed1f2e7b/OceanDNA-b46536.fa --refList OceanDNA-b46536/target_genomes.txt --output OceanDNA-b46536/fastani_result.tsv --threads 1
[2023-03-16 09:49:52,241] [INFO] Task succeeded: fastANI
[2023-03-16 09:49:52,241] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg930a004c-e1ae-421f-a062-b02f733b9a60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 09:49:52,242] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg930a004c-e1ae-421f-a062-b02f733b9a60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 09:49:52,242] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 09:49:52,242] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 09:49:52,242] [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
--------------------------------------------------------------------------------
[2023-03-16 09:49:52,243] [INFO] DFAST Taxonomy check result was written to OceanDNA-b46536/tc_result.tsv
[2023-03-16 09:49:52,246] [INFO] ===== Taxonomy check completed =====
[2023-03-16 09:49:52,246] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 09:49:52,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg930a004c-e1ae-421f-a062-b02f733b9a60/dqc_reference/checkm_data
[2023-03-16 09:49:52,249] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 09:49:52,264] [INFO] Task started: CheckM
[2023-03-16 09:49:52,264] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b46536/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b46536/checkm_input OceanDNA-b46536/checkm_result
[2023-03-16 09:50:40,068] [INFO] Task succeeded: CheckM
[2023-03-16 09:50:40,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 1.39%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-16 09:50:40,161] [INFO] ===== Completeness check finished =====
[2023-03-16 09:50:40,161] [INFO] ===== Start GTDB Search =====
[2023-03-16 09:50:40,161] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b46536/markers.fasta)
[2023-03-16 09:50:40,162] [INFO] Task started: Blastn
[2023-03-16 09:50:40,162] [INFO] Running command: blastn -query OceanDNA-b46536/markers.fasta -db /var/lib/cwl/stg930a004c-e1ae-421f-a062-b02f733b9a60/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b46536/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 09:50:40,859] [INFO] Task succeeded: Blastn
[2023-03-16 09:50:40,865] [INFO] Selected 15 target genomes.
[2023-03-16 09:50:40,866] [INFO] Target genome list was writen to OceanDNA-b46536/target_genomes_gtdb.txt
[2023-03-16 09:50:40,919] [INFO] Task started: fastANI
[2023-03-16 09:50:40,919] [INFO] Running command: fastANI --query /var/lib/cwl/stg8e3156e2-1362-4a28-aec2-1583ed1f2e7b/OceanDNA-b46536.fa --refList OceanDNA-b46536/target_genomes_gtdb.txt --output OceanDNA-b46536/fastani_result_gtdb.tsv --threads 1
[2023-03-16 09:50:49,992] [INFO] Task succeeded: fastANI
[2023-03-16 09:50:49,997] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 09:50:49,998] [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_015660155.1	s__JACNJL01 sp015660155	88.9616	313	554	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__JACNJL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014239365.1	s__JACNJL01 sp014239365	87.2897	502	554	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__JACNJL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382585.1	s__JACNJL01 sp014382585	85.5655	476	554	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__JACNJL01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002718935.1	s__UBA1100 sp002718935	77.7998	127	554	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA1100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002721895.1	s__UBA6614 sp002721895	77.6098	106	554	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA6614	95.0	97.45	95.11	0.88	0.86	3	-
GCA_011523245.1	s__UBA1100 sp011523245	77.44	110	554	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__UBA1100	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009695465.1	s__SYLI01 sp009695465	76.2356	80	554	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__UBA1100;g__SYLI01	95.0	99.82	99.82	0.91	0.91	2	-
GCA_009922615.1	s__SXTU01 sp009922615	75.543	55	554	d__Bacteria;p__Verrucomicrobiota;c__Verrucomicrobiae;o__Pedosphaerales;f__SXTU01;g__SXTU01	95.0	99.88	99.88	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2023-03-16 09:50:50,000] [INFO] GTDB search result was written to OceanDNA-b46536/result_gtdb.tsv
[2023-03-16 09:50:50,003] [INFO] ===== GTDB Search completed =====
[2023-03-16 09:50:50,007] [INFO] DFAST_QC result json was written to OceanDNA-b46536/dqc_result.json
[2023-03-16 09:50:50,007] [INFO] DFAST_QC completed!
[2023-03-16 09:50:50,007] [INFO] Total running time: 0h1m30s