[2023-03-18 09:27:55,567] [INFO] DFAST_QC pipeline started.
[2023-03-18 09:27:55,567] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 09:27:55,567] [INFO] DQC Reference Directory: /var/lib/cwl/stgcd6c7bc0-b78e-40c3-a578-d34f3cc620dd/dqc_reference
[2023-03-18 09:27:56,663] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 09:27:56,663] [INFO] Task started: Prodigal
[2023-03-18 09:27:56,663] [INFO] Running command: cat /var/lib/cwl/stg828c8f33-cd81-4a36-923a-99d9be159643/OceanDNA-b4388.fa | prodigal -d OceanDNA-b4388/cds.fna -a OceanDNA-b4388/protein.faa -g 11 -q > /dev/null
[2023-03-18 09:28:02,842] [INFO] Task succeeded: Prodigal
[2023-03-18 09:28:02,842] [INFO] Task started: HMMsearch
[2023-03-18 09:28:02,842] [INFO] Running command: hmmsearch --tblout OceanDNA-b4388/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcd6c7bc0-b78e-40c3-a578-d34f3cc620dd/dqc_reference/reference_markers.hmm OceanDNA-b4388/protein.faa > /dev/null
[2023-03-18 09:28:02,968] [INFO] Task succeeded: HMMsearch
[2023-03-18 09:28:02,968] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg828c8f33-cd81-4a36-923a-99d9be159643/OceanDNA-b4388.fa]
[2023-03-18 09:28:02,978] [INFO] Query marker FASTA was written to OceanDNA-b4388/markers.fasta
[2023-03-18 09:28:02,979] [INFO] Task started: Blastn
[2023-03-18 09:28:02,979] [INFO] Running command: blastn -query OceanDNA-b4388/markers.fasta -db /var/lib/cwl/stgcd6c7bc0-b78e-40c3-a578-d34f3cc620dd/dqc_reference/reference_markers.fasta -out OceanDNA-b4388/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:28:03,418] [INFO] Task succeeded: Blastn
[2023-03-18 09:28:03,419] [INFO] Selected 15 target genomes.
[2023-03-18 09:28:03,419] [INFO] Target genome list was writen to OceanDNA-b4388/target_genomes.txt
[2023-03-18 09:28:03,428] [INFO] Task started: fastANI
[2023-03-18 09:28:03,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg828c8f33-cd81-4a36-923a-99d9be159643/OceanDNA-b4388.fa --refList OceanDNA-b4388/target_genomes.txt --output OceanDNA-b4388/fastani_result.tsv --threads 1
[2023-03-18 09:28:10,672] [INFO] Task succeeded: fastANI
[2023-03-18 09:28:10,672] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcd6c7bc0-b78e-40c3-a578-d34f3cc620dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 09:28:10,673] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcd6c7bc0-b78e-40c3-a578-d34f3cc620dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 09:28:10,673] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 09:28:10,673] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 09:28:10,673] [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 09:28:10,673] [INFO] DFAST Taxonomy check result was written to OceanDNA-b4388/tc_result.tsv
[2023-03-18 09:28:10,673] [INFO] ===== Taxonomy check completed =====
[2023-03-18 09:28:10,673] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 09:28:10,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcd6c7bc0-b78e-40c3-a578-d34f3cc620dd/dqc_reference/checkm_data
[2023-03-18 09:28:10,676] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 09:28:10,679] [INFO] Task started: CheckM
[2023-03-18 09:28:10,679] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b4388/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b4388/checkm_input OceanDNA-b4388/checkm_result
[2023-03-18 09:28:31,691] [INFO] Task succeeded: CheckM
[2023-03-18 09:28:31,692] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 59.72%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 09:28:31,694] [INFO] ===== Completeness check finished =====
[2023-03-18 09:28:31,694] [INFO] ===== Start GTDB Search =====
[2023-03-18 09:28:31,694] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b4388/markers.fasta)
[2023-03-18 09:28:31,695] [INFO] Task started: Blastn
[2023-03-18 09:28:31,695] [INFO] Running command: blastn -query OceanDNA-b4388/markers.fasta -db /var/lib/cwl/stgcd6c7bc0-b78e-40c3-a578-d34f3cc620dd/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b4388/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 09:28:32,223] [INFO] Task succeeded: Blastn
[2023-03-18 09:28:32,224] [INFO] Selected 11 target genomes.
[2023-03-18 09:28:32,224] [INFO] Target genome list was writen to OceanDNA-b4388/target_genomes_gtdb.txt
[2023-03-18 09:28:32,303] [INFO] Task started: fastANI
[2023-03-18 09:28:32,303] [INFO] Running command: fastANI --query /var/lib/cwl/stg828c8f33-cd81-4a36-923a-99d9be159643/OceanDNA-b4388.fa --refList OceanDNA-b4388/target_genomes_gtdb.txt --output OceanDNA-b4388/fastani_result_gtdb.tsv --threads 1
[2023-03-18 09:28:35,291] [INFO] Task succeeded: fastANI
[2023-03-18 09:28:35,297] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 09:28:35,298] [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_002697405.1	s__MED-G16 sp002697405	97.8789	247	341	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	98.03	98.03	0.62	0.62	2	conclusive
GCA_902634135.1	s__MED-G16 sp902634135	82.9592	163	341	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902626505.1	s__MED-G16 sp902626505	82.3586	214	341	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002701745.1	s__MED-G16 sp002701745	82.2201	209	341	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	96.78	96.78	0.79	0.79	2	-
GCA_002457315.1	s__MED-G16 sp002457315	79.0979	169	341	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902523065.1	s__MED-G16 sp902523065	77.6018	126	341	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	96.84	95.61	0.92	0.88	9	-
GCA_902628365.1	s__GCA-2715645 sp902628365	77.5667	64	341	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__GCA-2715645	95.0	97.14	96.28	0.66	0.65	3	-
GCA_002692105.1	s__MED-G16 sp002692105	77.3079	106	341	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	97.44	97.02	0.77	0.72	3	-
GCA_902633975.1	s__MED-G16 sp902633975	77.1952	109	341	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__MED-G16;g__MED-G16	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 09:28:35,298] [INFO] GTDB search result was written to OceanDNA-b4388/result_gtdb.tsv
[2023-03-18 09:28:35,298] [INFO] ===== GTDB Search completed =====
[2023-03-18 09:28:35,299] [INFO] DFAST_QC result json was written to OceanDNA-b4388/dqc_result.json
[2023-03-18 09:28:35,299] [INFO] DFAST_QC completed!
[2023-03-18 09:28:35,299] [INFO] Total running time: 0h0m40s