[2023-03-14 11:36:02,655] [INFO] DFAST_QC pipeline started.
[2023-03-14 11:36:02,655] [INFO] DFAST_QC version: 0.5.7
[2023-03-14 11:36:02,655] [INFO] DQC Reference Directory: /var/lib/cwl/stge268ba2f-217f-412d-b0d1-c954e4f27735/dqc_reference
[2023-03-14 11:36:04,406] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-14 11:36:04,406] [INFO] Task started: Prodigal
[2023-03-14 11:36:04,406] [INFO] Running command: cat /var/lib/cwl/stg69a80961-dc01-4c39-aa22-314bd87fad2f/OceanDNA-b45088.fa | prodigal -d OceanDNA-b45088/cds.fna -a OceanDNA-b45088/protein.faa -g 11 -q > /dev/null
[2023-03-14 11:36:14,516] [INFO] Task succeeded: Prodigal
[2023-03-14 11:36:14,516] [INFO] Task started: HMMsearch
[2023-03-14 11:36:14,516] [INFO] Running command: hmmsearch --tblout OceanDNA-b45088/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge268ba2f-217f-412d-b0d1-c954e4f27735/dqc_reference/reference_markers.hmm OceanDNA-b45088/protein.faa > /dev/null
[2023-03-14 11:36:14,697] [INFO] Task succeeded: HMMsearch
[2023-03-14 11:36:14,698] [INFO] Found 6/6 markers.
[2023-03-14 11:36:14,717] [INFO] Query marker FASTA was written to OceanDNA-b45088/markers.fasta
[2023-03-14 11:36:14,719] [INFO] Task started: Blastn
[2023-03-14 11:36:14,719] [INFO] Running command: blastn -query OceanDNA-b45088/markers.fasta -db /var/lib/cwl/stge268ba2f-217f-412d-b0d1-c954e4f27735/dqc_reference/reference_markers.fasta -out OceanDNA-b45088/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:36:15,223] [INFO] Task succeeded: Blastn
[2023-03-14 11:36:15,224] [INFO] Selected 17 target genomes.
[2023-03-14 11:36:15,224] [INFO] Target genome list was writen to OceanDNA-b45088/target_genomes.txt
[2023-03-14 11:36:15,231] [INFO] Task started: fastANI
[2023-03-14 11:36:15,231] [INFO] Running command: fastANI --query /var/lib/cwl/stg69a80961-dc01-4c39-aa22-314bd87fad2f/OceanDNA-b45088.fa --refList OceanDNA-b45088/target_genomes.txt --output OceanDNA-b45088/fastani_result.tsv --threads 1
[2023-03-14 11:36:25,660] [INFO] Task succeeded: fastANI
[2023-03-14 11:36:25,661] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge268ba2f-217f-412d-b0d1-c954e4f27735/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-14 11:36:25,661] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge268ba2f-217f-412d-b0d1-c954e4f27735/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-14 11:36:25,661] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-14 11:36:25,661] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-14 11:36:25,661] [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 11:36:25,662] [INFO] DFAST Taxonomy check result was written to OceanDNA-b45088/tc_result.tsv
[2023-03-14 11:36:25,662] [INFO] ===== Taxonomy check completed =====
[2023-03-14 11:36:25,662] [INFO] ===== Start completeness check using CheckM =====
[2023-03-14 11:36:25,663] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge268ba2f-217f-412d-b0d1-c954e4f27735/dqc_reference/checkm_data
[2023-03-14 11:36:25,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-14 11:36:25,672] [INFO] Task started: CheckM
[2023-03-14 11:36:25,672] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b45088/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b45088/checkm_input OceanDNA-b45088/checkm_result
[2023-03-14 11:36:57,032] [INFO] Task succeeded: CheckM
[2023-03-14 11:36:57,032] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.02%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-14 11:36:57,035] [INFO] ===== Completeness check finished =====
[2023-03-14 11:36:57,035] [INFO] ===== Start GTDB Search =====
[2023-03-14 11:36:57,035] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b45088/markers.fasta)
[2023-03-14 11:36:57,036] [INFO] Task started: Blastn
[2023-03-14 11:36:57,036] [INFO] Running command: blastn -query OceanDNA-b45088/markers.fasta -db /var/lib/cwl/stge268ba2f-217f-412d-b0d1-c954e4f27735/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b45088/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-14 11:36:57,757] [INFO] Task succeeded: Blastn
[2023-03-14 11:36:57,758] [INFO] Selected 10 target genomes.
[2023-03-14 11:36:57,758] [INFO] Target genome list was writen to OceanDNA-b45088/target_genomes_gtdb.txt
[2023-03-14 11:36:57,857] [INFO] Task started: fastANI
[2023-03-14 11:36:57,858] [INFO] Running command: fastANI --query /var/lib/cwl/stg69a80961-dc01-4c39-aa22-314bd87fad2f/OceanDNA-b45088.fa --refList OceanDNA-b45088/target_genomes_gtdb.txt --output OceanDNA-b45088/fastani_result_gtdb.tsv --threads 1
[2023-03-14 11:37:02,960] [INFO] Task succeeded: fastANI
[2023-03-14 11:37:02,965] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-14 11:37:02,965] [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_011522845.1	s__JCVI-SCAAA005 sp011522845	97.6486	354	392	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002730365.1	s__JCVI-SCAAA005 sp002730365	92.5561	201	392	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002450295.1	s__JCVI-SCAAA005 sp002450295	90.0241	308	392	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	96.73	95.52	0.71	0.67	8	-
GCA_002683655.1	s__JCVI-SCAAA005 sp002683655	89.5467	290	392	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	98.22	98.15	0.75	0.71	3	-
GCA_003541985.1	s__JCVI-SCAAA005 sp003541985	85.5088	240	392	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000224765.2	s__JCVI-SCAAA005 sp000224765	85.1839	287	392	d__Bacteria;p__SAR324;c__SAR324;o__SAR324;f__NAC60-12;g__JCVI-SCAAA005	95.0	97.34	96.08	0.74	0.72	3	-
--------------------------------------------------------------------------------
[2023-03-14 11:37:02,965] [INFO] GTDB search result was written to OceanDNA-b45088/result_gtdb.tsv
[2023-03-14 11:37:02,966] [INFO] ===== GTDB Search completed =====
[2023-03-14 11:37:02,967] [INFO] DFAST_QC result json was written to OceanDNA-b45088/dqc_result.json
[2023-03-14 11:37:02,967] [INFO] DFAST_QC completed!
[2023-03-14 11:37:02,967] [INFO] Total running time: 0h1m0s