[2023-03-15 17:46:31,697] [INFO] DFAST_QC pipeline started.
[2023-03-15 17:46:31,697] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 17:46:31,698] [INFO] DQC Reference Directory: /var/lib/cwl/stg049b25d9-3c27-4f61-a817-e56e64d0bbd4/dqc_reference
[2023-03-15 17:46:32,771] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 17:46:32,772] [INFO] Task started: Prodigal
[2023-03-15 17:46:32,772] [INFO] Running command: cat /var/lib/cwl/stg3baecf24-21a6-4f1d-9d8c-a88609d2f415/OceanDNA-b11888.fa | prodigal -d OceanDNA-b11888/cds.fna -a OceanDNA-b11888/protein.faa -g 11 -q > /dev/null
[2023-03-15 17:46:52,648] [INFO] Task succeeded: Prodigal
[2023-03-15 17:46:52,648] [INFO] Task started: HMMsearch
[2023-03-15 17:46:52,648] [INFO] Running command: hmmsearch --tblout OceanDNA-b11888/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg049b25d9-3c27-4f61-a817-e56e64d0bbd4/dqc_reference/reference_markers.hmm OceanDNA-b11888/protein.faa > /dev/null
[2023-03-15 17:46:52,816] [INFO] Task succeeded: HMMsearch
[2023-03-15 17:46:52,816] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3baecf24-21a6-4f1d-9d8c-a88609d2f415/OceanDNA-b11888.fa]
[2023-03-15 17:46:52,836] [INFO] Query marker FASTA was written to OceanDNA-b11888/markers.fasta
[2023-03-15 17:46:52,838] [INFO] Task started: Blastn
[2023-03-15 17:46:52,838] [INFO] Running command: blastn -query OceanDNA-b11888/markers.fasta -db /var/lib/cwl/stg049b25d9-3c27-4f61-a817-e56e64d0bbd4/dqc_reference/reference_markers.fasta -out OceanDNA-b11888/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:46:53,356] [INFO] Task succeeded: Blastn
[2023-03-15 17:46:53,359] [INFO] Selected 29 target genomes.
[2023-03-15 17:46:53,360] [INFO] Target genome list was writen to OceanDNA-b11888/target_genomes.txt
[2023-03-15 17:46:53,375] [INFO] Task started: fastANI
[2023-03-15 17:46:53,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg3baecf24-21a6-4f1d-9d8c-a88609d2f415/OceanDNA-b11888.fa --refList OceanDNA-b11888/target_genomes.txt --output OceanDNA-b11888/fastani_result.tsv --threads 1
[2023-03-15 17:47:12,213] [INFO] Task succeeded: fastANI
[2023-03-15 17:47:12,214] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg049b25d9-3c27-4f61-a817-e56e64d0bbd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 17:47:12,214] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg049b25d9-3c27-4f61-a817-e56e64d0bbd4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 17:47:12,214] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 17:47:12,214] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 17:47:12,214] [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
--------------------------------------------------------------------------------
[2023-03-15 17:47:12,215] [INFO] DFAST Taxonomy check result was written to OceanDNA-b11888/tc_result.tsv
[2023-03-15 17:47:12,215] [INFO] ===== Taxonomy check completed =====
[2023-03-15 17:47:12,215] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 17:47:12,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg049b25d9-3c27-4f61-a817-e56e64d0bbd4/dqc_reference/checkm_data
[2023-03-15 17:47:12,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 17:47:12,291] [INFO] Task started: CheckM
[2023-03-15 17:47:12,291] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b11888/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b11888/checkm_input OceanDNA-b11888/checkm_result
[2023-03-15 17:48:12,496] [INFO] Task succeeded: CheckM
[2023-03-15 17:48:12,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 1.30%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-15 17:48:12,499] [INFO] ===== Completeness check finished =====
[2023-03-15 17:48:12,499] [INFO] ===== Start GTDB Search =====
[2023-03-15 17:48:12,499] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b11888/markers.fasta)
[2023-03-15 17:48:12,500] [INFO] Task started: Blastn
[2023-03-15 17:48:12,501] [INFO] Running command: blastn -query OceanDNA-b11888/markers.fasta -db /var/lib/cwl/stg049b25d9-3c27-4f61-a817-e56e64d0bbd4/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b11888/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 17:48:13,259] [INFO] Task succeeded: Blastn
[2023-03-15 17:48:13,260] [INFO] Selected 20 target genomes.
[2023-03-15 17:48:13,260] [INFO] Target genome list was writen to OceanDNA-b11888/target_genomes_gtdb.txt
[2023-03-15 17:48:13,285] [INFO] Task started: fastANI
[2023-03-15 17:48:13,285] [INFO] Running command: fastANI --query /var/lib/cwl/stg3baecf24-21a6-4f1d-9d8c-a88609d2f415/OceanDNA-b11888.fa --refList OceanDNA-b11888/target_genomes_gtdb.txt --output OceanDNA-b11888/fastani_result_gtdb.tsv --threads 1
[2023-03-15 17:48:21,098] [INFO] Task succeeded: fastANI
[2023-03-15 17:48:21,103] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-15 17:48:21,103] [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_002683345.1	s__UBA11663 sp002683345	79.9754	211	556	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002863145.1	s__UBA11663 sp002863145	79.2645	236	556	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	97.56	96.60	0.84	0.82	6	-
GCA_011524845.1	s__UBA11663 sp011524845	79.0857	194	556	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002729115.1	s__UBA11663 sp002729115	78.6845	172	556	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	96.51	95.05	0.71	0.69	4	-
GCA_002313415.1	s__UBA11663 sp002313415	77.7632	95	556	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	99.13	99.10	0.82	0.81	3	-
GCA_002469765.1	s__UBA11663 sp002469765	77.615	165	556	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UBA11663	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002863125.1	s__UA16 sp002863125	76.3191	71	556	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__UA16;g__UA16	95.0	97.01	95.79	0.91	0.89	5	-
--------------------------------------------------------------------------------
[2023-03-15 17:48:21,117] [INFO] GTDB search result was written to OceanDNA-b11888/result_gtdb.tsv
[2023-03-15 17:48:21,117] [INFO] ===== GTDB Search completed =====
[2023-03-15 17:48:21,117] [INFO] DFAST_QC result json was written to OceanDNA-b11888/dqc_result.json
[2023-03-15 17:48:21,118] [INFO] DFAST_QC completed!
[2023-03-15 17:48:21,118] [INFO] Total running time: 0h1m49s