[2023-03-17 23:39:58,820] [INFO] DFAST_QC pipeline started.
[2023-03-17 23:39:58,820] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 23:39:58,820] [INFO] DQC Reference Directory: /var/lib/cwl/stg7ec0305b-bd51-4c01-b17e-e2cd8ce8e7aa/dqc_reference
[2023-03-17 23:39:59,972] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 23:39:59,972] [INFO] Task started: Prodigal
[2023-03-17 23:39:59,973] [INFO] Running command: cat /var/lib/cwl/stg4138e3c0-e37a-4272-972e-6fc475c3d9e2/OceanDNA-b44718.fa | prodigal -d OceanDNA-b44718/cds.fna -a OceanDNA-b44718/protein.faa -g 11 -q > /dev/null
[2023-03-17 23:40:12,928] [INFO] Task succeeded: Prodigal
[2023-03-17 23:40:12,928] [INFO] Task started: HMMsearch
[2023-03-17 23:40:12,928] [INFO] Running command: hmmsearch --tblout OceanDNA-b44718/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7ec0305b-bd51-4c01-b17e-e2cd8ce8e7aa/dqc_reference/reference_markers.hmm OceanDNA-b44718/protein.faa > /dev/null
[2023-03-17 23:40:13,114] [INFO] Task succeeded: HMMsearch
[2023-03-17 23:40:13,114] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4138e3c0-e37a-4272-972e-6fc475c3d9e2/OceanDNA-b44718.fa]
[2023-03-17 23:40:13,132] [INFO] Query marker FASTA was written to OceanDNA-b44718/markers.fasta
[2023-03-17 23:40:13,133] [INFO] Task started: Blastn
[2023-03-17 23:40:13,133] [INFO] Running command: blastn -query OceanDNA-b44718/markers.fasta -db /var/lib/cwl/stg7ec0305b-bd51-4c01-b17e-e2cd8ce8e7aa/dqc_reference/reference_markers.fasta -out OceanDNA-b44718/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:40:13,640] [INFO] Task succeeded: Blastn
[2023-03-17 23:40:13,641] [INFO] Selected 9 target genomes.
[2023-03-17 23:40:13,641] [INFO] Target genome list was writen to OceanDNA-b44718/target_genomes.txt
[2023-03-17 23:40:13,700] [INFO] Task started: fastANI
[2023-03-17 23:40:13,700] [INFO] Running command: fastANI --query /var/lib/cwl/stg4138e3c0-e37a-4272-972e-6fc475c3d9e2/OceanDNA-b44718.fa --refList OceanDNA-b44718/target_genomes.txt --output OceanDNA-b44718/fastani_result.tsv --threads 1
[2023-03-17 23:40:17,641] [INFO] Task succeeded: fastANI
[2023-03-17 23:40:17,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7ec0305b-bd51-4c01-b17e-e2cd8ce8e7aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 23:40:17,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7ec0305b-bd51-4c01-b17e-e2cd8ce8e7aa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 23:40:17,642] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 23:40:17,642] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 23:40:17,642] [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
--------------------------------------------------------------------------------
[2023-03-17 23:40:17,642] [INFO] DFAST Taxonomy check result was written to OceanDNA-b44718/tc_result.tsv
[2023-03-17 23:40:17,642] [INFO] ===== Taxonomy check completed =====
[2023-03-17 23:40:17,642] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 23:40:17,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7ec0305b-bd51-4c01-b17e-e2cd8ce8e7aa/dqc_reference/checkm_data
[2023-03-17 23:40:17,645] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 23:40:17,649] [INFO] Task started: CheckM
[2023-03-17 23:40:17,649] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b44718/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b44718/checkm_input OceanDNA-b44718/checkm_result
[2023-03-17 23:40:55,826] [INFO] Task succeeded: CheckM
[2023-03-17 23:40:55,827] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 23:40:55,829] [INFO] ===== Completeness check finished =====
[2023-03-17 23:40:55,829] [INFO] ===== Start GTDB Search =====
[2023-03-17 23:40:55,829] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b44718/markers.fasta)
[2023-03-17 23:40:55,830] [INFO] Task started: Blastn
[2023-03-17 23:40:55,830] [INFO] Running command: blastn -query OceanDNA-b44718/markers.fasta -db /var/lib/cwl/stg7ec0305b-bd51-4c01-b17e-e2cd8ce8e7aa/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b44718/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 23:40:56,528] [INFO] Task succeeded: Blastn
[2023-03-17 23:40:56,531] [INFO] Selected 16 target genomes.
[2023-03-17 23:40:56,531] [INFO] Target genome list was writen to OceanDNA-b44718/target_genomes_gtdb.txt
[2023-03-17 23:40:56,767] [INFO] Task started: fastANI
[2023-03-17 23:40:56,768] [INFO] Running command: fastANI --query /var/lib/cwl/stg4138e3c0-e37a-4272-972e-6fc475c3d9e2/OceanDNA-b44718.fa --refList OceanDNA-b44718/target_genomes_gtdb.txt --output OceanDNA-b44718/fastani_result_gtdb.tsv --threads 1
[2023-03-17 23:41:05,694] [INFO] Task succeeded: fastANI
[2023-03-17 23:41:05,698] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 23:41:05,699] [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_902562015.1	s__Arctic96AD-7 sp902562015	85.0294	196	417	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902564345.1	s__Arctic96AD-7 sp902564345	82.0099	204	417	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	98.84	98.84	0.77	0.77	2	-
GCA_002716165.1	s__Arctic96AD-7 sp002716165	81.5564	196	417	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001627865.1	s__Arctic96AD-7 sp001627865	80.3291	332	417	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	99.71	99.45	0.95	0.94	9	-
GCA_002082305.1	s__Arctic96AD-7 sp002082305	76.9592	118	417	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	98.68	95.22	0.86	0.64	13	-
GCA_016764995.1	s__Arctic96AD-7 sp016764995	76.5026	91	417	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002685535.1	s__Arctic96AD-7 sp002685535	76.2475	78	417	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__Arctic96AD-7	95.0	97.44	95.94	0.78	0.68	5	-
--------------------------------------------------------------------------------
[2023-03-17 23:41:05,700] [INFO] GTDB search result was written to OceanDNA-b44718/result_gtdb.tsv
[2023-03-17 23:41:05,700] [INFO] ===== GTDB Search completed =====
[2023-03-17 23:41:05,701] [INFO] DFAST_QC result json was written to OceanDNA-b44718/dqc_result.json
[2023-03-17 23:41:05,701] [INFO] DFAST_QC completed!
[2023-03-17 23:41:05,701] [INFO] Total running time: 0h1m7s