[2023-03-14 14:20:15,973] [INFO] DFAST_QC pipeline started.
[2023-03-14 14:20:15,973] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 14:20:15,973] [INFO] DQC Reference Directory: /var/lib/cwl/stg98994dda-c2e9-4f91-9ad7-385c5065550f/dqc_reference
[2023-03-14 14:20:18,690] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 14:20:18,691] [INFO] Task started: Prodigal
[2023-03-14 14:20:18,691] [INFO] Running command: cat /var/lib/cwl/stg95c4b0d4-f3c7-4e3f-9bda-568e9fede3ec/OceanDNA-b18031.fa | prodigal -d OceanDNA-b18031/cds.fna -a OceanDNA-b18031/protein.faa -g 11 -q > /dev/null
[2023-03-14 14:20:22,999] [INFO] Task succeeded: Prodigal
[2023-03-14 14:20:23,000] [INFO] Task started: HMMsearch
[2023-03-14 14:20:23,000] [INFO] Running command: hmmsearch --tblout OceanDNA-b18031/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg98994dda-c2e9-4f91-9ad7-385c5065550f/dqc_reference/reference_markers.hmm OceanDNA-b18031/protein.faa > /dev/null
[2023-03-14 14:20:23,184] [INFO] Task succeeded: HMMsearch
[2023-03-14 14:20:23,184] [INFO] Found 6/6 markers.
[2023-03-14 14:20:23,192] [INFO] Query marker FASTA was written to OceanDNA-b18031/markers.fasta
[2023-03-14 14:20:23,195] [INFO] Task started: Blastn
[2023-03-14 14:20:23,195] [INFO] Running command: blastn -query OceanDNA-b18031/markers.fasta -db /var/lib/cwl/stg98994dda-c2e9-4f91-9ad7-385c5065550f/dqc_reference/reference_markers.fasta -out OceanDNA-b18031/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:20:23,851] [INFO] Task succeeded: Blastn
[2023-03-14 14:20:23,852] [INFO] Selected 22 target genomes.
[2023-03-14 14:20:23,852] [INFO] Target genome list was writen to OceanDNA-b18031/target_genomes.txt
[2023-03-14 14:20:23,956] [INFO] Task started: fastANI
[2023-03-14 14:20:23,956] [INFO] Running command: fastANI --query /var/lib/cwl/stg95c4b0d4-f3c7-4e3f-9bda-568e9fede3ec/OceanDNA-b18031.fa --refList OceanDNA-b18031/target_genomes.txt --output OceanDNA-b18031/fastani_result.tsv --threads 1
[2023-03-14 14:20:34,427] [INFO] Task succeeded: fastANI
[2023-03-14 14:20:34,428] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg98994dda-c2e9-4f91-9ad7-385c5065550f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 14:20:34,428] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg98994dda-c2e9-4f91-9ad7-385c5065550f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 14:20:34,428] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 14:20:34,428] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 14:20:34,429] [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
--------------------------------------------------------------------------------
[2023-03-14 14:20:34,429] [INFO] DFAST Taxonomy check result was written to OceanDNA-b18031/tc_result.tsv
[2023-03-14 14:20:34,429] [INFO] ===== Taxonomy check completed =====
[2023-03-14 14:20:34,429] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 14:20:34,429] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg98994dda-c2e9-4f91-9ad7-385c5065550f/dqc_reference/checkm_data
[2023-03-14 14:20:34,432] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 14:20:34,486] [INFO] Task started: CheckM
[2023-03-14 14:20:34,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b18031/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b18031/checkm_input OceanDNA-b18031/checkm_result
[2023-03-14 14:20:57,029] [INFO] Task succeeded: CheckM
[2023-03-14 14:20:57,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 90.62%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 14:20:57,031] [INFO] ===== Completeness check finished =====
[2023-03-14 14:20:57,032] [INFO] ===== Start GTDB Search =====
[2023-03-14 14:20:57,032] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b18031/markers.fasta)
[2023-03-14 14:20:57,033] [INFO] Task started: Blastn
[2023-03-14 14:20:57,033] [INFO] Running command: blastn -query OceanDNA-b18031/markers.fasta -db /var/lib/cwl/stg98994dda-c2e9-4f91-9ad7-385c5065550f/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b18031/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 14:20:58,761] [INFO] Task succeeded: Blastn
[2023-03-14 14:20:58,763] [INFO] Selected 10 target genomes.
[2023-03-14 14:20:58,763] [INFO] Target genome list was writen to OceanDNA-b18031/target_genomes_gtdb.txt
[2023-03-14 14:20:58,794] [INFO] Task started: fastANI
[2023-03-14 14:20:58,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg95c4b0d4-f3c7-4e3f-9bda-568e9fede3ec/OceanDNA-b18031.fa --refList OceanDNA-b18031/target_genomes_gtdb.txt --output OceanDNA-b18031/fastani_result_gtdb.tsv --threads 1
[2023-03-14 14:21:01,763] [INFO] Task succeeded: fastANI
[2023-03-14 14:21:01,769] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-14 14:21:01,770] [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_014240005.1	s__Marinisoma sp014240005	84.3005	148	194	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.63	96.63	0.87	0.87	2	-
GCA_002701645.1	s__Marinisoma sp002701645	83.7153	138	194	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182795.1	s__Marinisoma sp905182795	82.6899	170	194	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000402755.1	s__Marinisoma sp000402755	82.5204	157	194	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	95.42	95.16	0.79	0.76	17	-
GCA_000402815.1	s__Marinisoma atlanticum	81.2218	158	194	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.54	99.22	0.95	0.89	4	-
GCA_002348725.1	s__Marinisoma sp002348725	78.5116	69	194	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.66	99.62	0.84	0.83	4	-
GCA_000402655.1	s__Marinisoma sp000402655	78.0994	69	194	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.42	95.83	0.93	0.92	4	-
GCA_902624275.1	s__Marinisoma sp902624275	77.6895	64	194	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012963075.1	s__Marinisoma sp012963075	76.6515	51	194	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-14 14:21:01,770] [INFO] GTDB search result was written to OceanDNA-b18031/result_gtdb.tsv
[2023-03-14 14:21:01,770] [INFO] ===== GTDB Search completed =====
[2023-03-14 14:21:01,772] [INFO] DFAST_QC result json was written to OceanDNA-b18031/dqc_result.json
[2023-03-14 14:21:01,772] [INFO] DFAST_QC completed!
[2023-03-14 14:21:01,772] [INFO] Total running time: 0h0m46s