[2023-03-18 23:45:35,840] [INFO] DFAST_QC pipeline started.
[2023-03-18 23:45:35,840] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 23:45:35,840] [INFO] DQC Reference Directory: /var/lib/cwl/stg8a061b90-561a-4b2f-b947-cf94d0064f04/dqc_reference
[2023-03-18 23:45:37,728] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 23:45:37,729] [INFO] Task started: Prodigal
[2023-03-18 23:45:37,729] [INFO] Running command: cat /var/lib/cwl/stg63c43105-95f0-4a20-89b7-1b17091cdb97/OceanDNA-b21343.fa | prodigal -d OceanDNA-b21343/cds.fna -a OceanDNA-b21343/protein.faa -g 11 -q > /dev/null
[2023-03-18 23:45:52,101] [INFO] Task succeeded: Prodigal
[2023-03-18 23:45:52,101] [INFO] Task started: HMMsearch
[2023-03-18 23:45:52,102] [INFO] Running command: hmmsearch --tblout OceanDNA-b21343/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8a061b90-561a-4b2f-b947-cf94d0064f04/dqc_reference/reference_markers.hmm OceanDNA-b21343/protein.faa > /dev/null
[2023-03-18 23:45:52,310] [INFO] Task succeeded: HMMsearch
[2023-03-18 23:45:52,310] [INFO] Found 6/6 markers.
[2023-03-18 23:45:52,328] [INFO] Query marker FASTA was written to OceanDNA-b21343/markers.fasta
[2023-03-18 23:45:52,329] [INFO] Task started: Blastn
[2023-03-18 23:45:52,329] [INFO] Running command: blastn -query OceanDNA-b21343/markers.fasta -db /var/lib/cwl/stg8a061b90-561a-4b2f-b947-cf94d0064f04/dqc_reference/reference_markers.fasta -out OceanDNA-b21343/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:45:52,900] [INFO] Task succeeded: Blastn
[2023-03-18 23:45:52,901] [INFO] Selected 19 target genomes.
[2023-03-18 23:45:52,901] [INFO] Target genome list was writen to OceanDNA-b21343/target_genomes.txt
[2023-03-18 23:45:52,911] [INFO] Task started: fastANI
[2023-03-18 23:45:52,911] [INFO] Running command: fastANI --query /var/lib/cwl/stg63c43105-95f0-4a20-89b7-1b17091cdb97/OceanDNA-b21343.fa --refList OceanDNA-b21343/target_genomes.txt --output OceanDNA-b21343/fastani_result.tsv --threads 1
[2023-03-18 23:46:02,852] [INFO] Task succeeded: fastANI
[2023-03-18 23:46:02,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8a061b90-561a-4b2f-b947-cf94d0064f04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 23:46:02,853] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8a061b90-561a-4b2f-b947-cf94d0064f04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 23:46:02,853] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 23:46:02,853] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 23:46:02,853] [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
--------------------------------------------------------------------------------
[2023-03-18 23:46:02,853] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21343/tc_result.tsv
[2023-03-18 23:46:02,853] [INFO] ===== Taxonomy check completed =====
[2023-03-18 23:46:02,854] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 23:46:02,854] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8a061b90-561a-4b2f-b947-cf94d0064f04/dqc_reference/checkm_data
[2023-03-18 23:46:02,857] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 23:46:02,908] [INFO] Task started: CheckM
[2023-03-18 23:46:02,908] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21343/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21343/checkm_input OceanDNA-b21343/checkm_result
[2023-03-18 23:46:43,101] [INFO] Task succeeded: CheckM
[2023-03-18 23:46:43,101] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 23:46:43,104] [INFO] ===== Completeness check finished =====
[2023-03-18 23:46:43,104] [INFO] ===== Start GTDB Search =====
[2023-03-18 23:46:43,104] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21343/markers.fasta)
[2023-03-18 23:46:43,105] [INFO] Task started: Blastn
[2023-03-18 23:46:43,105] [INFO] Running command: blastn -query OceanDNA-b21343/markers.fasta -db /var/lib/cwl/stg8a061b90-561a-4b2f-b947-cf94d0064f04/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21343/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 23:46:44,003] [INFO] Task succeeded: Blastn
[2023-03-18 23:46:44,004] [INFO] Selected 22 target genomes.
[2023-03-18 23:46:44,004] [INFO] Target genome list was writen to OceanDNA-b21343/target_genomes_gtdb.txt
[2023-03-18 23:46:44,022] [INFO] Task started: fastANI
[2023-03-18 23:46:44,022] [INFO] Running command: fastANI --query /var/lib/cwl/stg63c43105-95f0-4a20-89b7-1b17091cdb97/OceanDNA-b21343.fa --refList OceanDNA-b21343/target_genomes_gtdb.txt --output OceanDNA-b21343/fastani_result_gtdb.tsv --threads 1
[2023-03-18 23:46:54,557] [INFO] Task succeeded: fastANI
[2023-03-18 23:46:54,564] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 23:46:54,565] [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_013349585.1	s__UBA8687 sp013349585	99.76	538	863	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016763735.1	s__UBA8687 sp016763735	89.749	246	863	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018665625.1	s__UBA8687 sp018665625	78.7366	362	863	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009873655.1	s__UBA8687 sp009873655	77.6865	311	863	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	99.50	99.47	0.94	0.93	3	-
GCA_002697825.1	s__UBA8687 sp002697825	77.1521	156	863	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018653085.1	s__LS-NOB sp018653085	76.7856	128	863	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.81	99.70	0.96	0.92	14	-
GCA_014382285.1	s__LS-NOB sp014382285	76.7716	95	863	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.85	99.85	0.92	0.92	2	-
GCA_002721515.1	s__UBA8687 sp002721515	76.6963	123	863	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__UBA8687	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009873635.1	s__LS-NOB sp009873635	76.6756	94	863	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.03	98.80	0.95	0.93	3	-
GCA_018673915.1	s__LS-NOB sp018673915	76.5747	112	863	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.92	99.88	0.94	0.90	12	-
GCA_002786505.1	s__LS-NOB sp002786505	76.3894	70	863	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018664975.1	s__LS-NOB sp018664975	76.041	74	863	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 23:46:54,565] [INFO] GTDB search result was written to OceanDNA-b21343/result_gtdb.tsv
[2023-03-18 23:46:54,565] [INFO] ===== GTDB Search completed =====
[2023-03-18 23:46:54,566] [INFO] DFAST_QC result json was written to OceanDNA-b21343/dqc_result.json
[2023-03-18 23:46:54,566] [INFO] DFAST_QC completed!
[2023-03-18 23:46:54,566] [INFO] Total running time: 0h1m19s