[2023-03-17 05:34:58,189] [INFO] DFAST_QC pipeline started.
[2023-03-17 05:34:58,189] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 05:34:58,190] [INFO] DQC Reference Directory: /var/lib/cwl/stg30d22707-09fe-45c5-9cab-d6b41a71964e/dqc_reference
[2023-03-17 05:34:59,284] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 05:34:59,284] [INFO] Task started: Prodigal
[2023-03-17 05:34:59,284] [INFO] Running command: cat /var/lib/cwl/stg4307d0fa-6a6b-4763-b0db-984bda5862df/OceanDNA-a4635.fa | prodigal -d OceanDNA-a4635/cds.fna -a OceanDNA-a4635/protein.faa -g 11 -q > /dev/null
[2023-03-17 05:35:06,193] [INFO] Task succeeded: Prodigal
[2023-03-17 05:35:06,193] [INFO] Task started: HMMsearch
[2023-03-17 05:35:06,193] [INFO] Running command: hmmsearch --tblout OceanDNA-a4635/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg30d22707-09fe-45c5-9cab-d6b41a71964e/dqc_reference/reference_markers.hmm OceanDNA-a4635/protein.faa > /dev/null
[2023-03-17 05:35:06,354] [INFO] Task succeeded: HMMsearch
[2023-03-17 05:35:06,354] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4307d0fa-6a6b-4763-b0db-984bda5862df/OceanDNA-a4635.fa]
[2023-03-17 05:35:06,375] [INFO] Query marker FASTA was written to OceanDNA-a4635/markers.fasta
[2023-03-17 05:35:06,376] [INFO] Task started: Blastn
[2023-03-17 05:35:06,376] [INFO] Running command: blastn -query OceanDNA-a4635/markers.fasta -db /var/lib/cwl/stg30d22707-09fe-45c5-9cab-d6b41a71964e/dqc_reference/reference_markers.fasta -out OceanDNA-a4635/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:35:06,809] [INFO] Task succeeded: Blastn
[2023-03-17 05:35:06,812] [INFO] Selected 1 target genomes.
[2023-03-17 05:35:06,812] [INFO] Target genome list was writen to OceanDNA-a4635/target_genomes.txt
[2023-03-17 05:35:06,813] [INFO] Task started: fastANI
[2023-03-17 05:35:06,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg4307d0fa-6a6b-4763-b0db-984bda5862df/OceanDNA-a4635.fa --refList OceanDNA-a4635/target_genomes.txt --output OceanDNA-a4635/fastani_result.tsv --threads 1
[2023-03-17 05:35:07,693] [INFO] Task succeeded: fastANI
[2023-03-17 05:35:07,693] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg30d22707-09fe-45c5-9cab-d6b41a71964e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 05:35:07,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg30d22707-09fe-45c5-9cab-d6b41a71964e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 05:35:07,694] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 05:35:07,694] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 05:35:07,694] [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 05:35:07,695] [INFO] DFAST Taxonomy check result was written to OceanDNA-a4635/tc_result.tsv
[2023-03-17 05:35:07,696] [INFO] ===== Taxonomy check completed =====
[2023-03-17 05:35:07,696] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 05:35:07,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg30d22707-09fe-45c5-9cab-d6b41a71964e/dqc_reference/checkm_data
[2023-03-17 05:35:07,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 05:35:08,113] [INFO] Task started: CheckM
[2023-03-17 05:35:08,113] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4635/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4635/checkm_input OceanDNA-a4635/checkm_result
[2023-03-17 05:35:31,040] [INFO] Task succeeded: CheckM
[2023-03-17 05:35:31,040] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.90%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 05:35:31,074] [INFO] ===== Completeness check finished =====
[2023-03-17 05:35:31,075] [INFO] ===== Start GTDB Search =====
[2023-03-17 05:35:31,075] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4635/markers.fasta)
[2023-03-17 05:35:31,076] [INFO] Task started: Blastn
[2023-03-17 05:35:31,076] [INFO] Running command: blastn -query OceanDNA-a4635/markers.fasta -db /var/lib/cwl/stg30d22707-09fe-45c5-9cab-d6b41a71964e/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4635/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 05:35:31,503] [INFO] Task succeeded: Blastn
[2023-03-17 05:35:31,506] [INFO] Selected 5 target genomes.
[2023-03-17 05:35:31,506] [INFO] Target genome list was writen to OceanDNA-a4635/target_genomes_gtdb.txt
[2023-03-17 05:35:31,513] [INFO] Task started: fastANI
[2023-03-17 05:35:31,513] [INFO] Running command: fastANI --query /var/lib/cwl/stg4307d0fa-6a6b-4763-b0db-984bda5862df/OceanDNA-a4635.fa --refList OceanDNA-a4635/target_genomes_gtdb.txt --output OceanDNA-a4635/fastani_result_gtdb.tsv --threads 1
[2023-03-17 05:35:33,090] [INFO] Task succeeded: fastANI
[2023-03-17 05:35:33,094] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-17 05:35:33,094] [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_002502095.1	s__MGIIb-O5 sp002502095	99.6484	361	409	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.50	98.52	0.89	0.78	6	conclusive
GCA_002501805.1	s__MGIIb-O5 sp002501805	93.6648	366	409	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	97.49	96.31	0.90	0.85	5	-
GCA_002499865.1	s__MGIIb-O5 sp002499865	90.6819	331	409	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.65	99.57	0.89	0.88	3	-
GCA_002499325.1	s__MGIIb-O5 sp002499325	90.481	297	409	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	99.30	99.30	0.84	0.84	2	-
GCA_002506825.1	s__MGIIb-O5 sp002506825	81.8927	302	409	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-O5	95.0	98.02	97.97	0.86	0.84	3	-
--------------------------------------------------------------------------------
[2023-03-17 05:35:33,097] [INFO] GTDB search result was written to OceanDNA-a4635/result_gtdb.tsv
[2023-03-17 05:35:33,102] [INFO] ===== GTDB Search completed =====
[2023-03-17 05:35:33,106] [INFO] DFAST_QC result json was written to OceanDNA-a4635/dqc_result.json
[2023-03-17 05:35:33,106] [INFO] DFAST_QC completed!
[2023-03-17 05:35:33,106] [INFO] Total running time: 0h0m35s