[2023-03-16 18:33:26,211] [INFO] DFAST_QC pipeline started.
[2023-03-16 18:33:26,211] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 18:33:26,211] [INFO] DQC Reference Directory: /var/lib/cwl/stgc3335c24-70d0-4b22-a029-e913bb4874d0/dqc_reference
[2023-03-16 18:33:28,079] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 18:33:28,080] [INFO] Task started: Prodigal
[2023-03-16 18:33:28,080] [INFO] Running command: cat /var/lib/cwl/stg0b30f257-ffdc-4678-9232-12cad272c9e4/OceanDNA-a2850.fa | prodigal -d OceanDNA-a2850/cds.fna -a OceanDNA-a2850/protein.faa -g 11 -q > /dev/null
[2023-03-16 18:33:46,760] [INFO] Task succeeded: Prodigal
[2023-03-16 18:33:46,760] [INFO] Task started: HMMsearch
[2023-03-16 18:33:46,760] [INFO] Running command: hmmsearch --tblout OceanDNA-a2850/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc3335c24-70d0-4b22-a029-e913bb4874d0/dqc_reference/reference_markers.hmm OceanDNA-a2850/protein.faa > /dev/null
[2023-03-16 18:33:46,926] [INFO] Task succeeded: HMMsearch
[2023-03-16 18:33:46,927] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg0b30f257-ffdc-4678-9232-12cad272c9e4/OceanDNA-a2850.fa]
[2023-03-16 18:33:46,944] [INFO] Query marker FASTA was written to OceanDNA-a2850/markers.fasta
[2023-03-16 18:33:46,946] [INFO] Task started: Blastn
[2023-03-16 18:33:46,946] [INFO] Running command: blastn -query OceanDNA-a2850/markers.fasta -db /var/lib/cwl/stgc3335c24-70d0-4b22-a029-e913bb4874d0/dqc_reference/reference_markers.fasta -out OceanDNA-a2850/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:33:47,401] [INFO] Task succeeded: Blastn
[2023-03-16 18:33:47,403] [INFO] Selected 5 target genomes.
[2023-03-16 18:33:47,403] [INFO] Target genome list was writen to OceanDNA-a2850/target_genomes.txt
[2023-03-16 18:33:47,407] [INFO] Task started: fastANI
[2023-03-16 18:33:47,407] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b30f257-ffdc-4678-9232-12cad272c9e4/OceanDNA-a2850.fa --refList OceanDNA-a2850/target_genomes.txt --output OceanDNA-a2850/fastani_result.tsv --threads 1
[2023-03-16 18:33:51,639] [INFO] Task succeeded: fastANI
[2023-03-16 18:33:51,640] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc3335c24-70d0-4b22-a029-e913bb4874d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 18:33:51,640] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc3335c24-70d0-4b22-a029-e913bb4874d0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 18:33:51,640] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 18:33:51,640] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 18:33:51,640] [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
--------------------------------------------------------------------------------
[2023-03-16 18:33:51,641] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2850/tc_result.tsv
[2023-03-16 18:33:51,641] [INFO] ===== Taxonomy check completed =====
[2023-03-16 18:33:51,642] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 18:33:51,642] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc3335c24-70d0-4b22-a029-e913bb4874d0/dqc_reference/checkm_data
[2023-03-16 18:33:51,691] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 18:33:51,702] [INFO] Task started: CheckM
[2023-03-16 18:33:51,702] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2850/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2850/checkm_input OceanDNA-a2850/checkm_result
[2023-03-16 18:34:35,249] [INFO] Task succeeded: CheckM
[2023-03-16 18:34:35,250] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 73.45%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 18:34:35,259] [INFO] ===== Completeness check finished =====
[2023-03-16 18:34:35,259] [INFO] ===== Start GTDB Search =====
[2023-03-16 18:34:35,260] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2850/markers.fasta)
[2023-03-16 18:34:35,261] [INFO] Task started: Blastn
[2023-03-16 18:34:35,261] [INFO] Running command: blastn -query OceanDNA-a2850/markers.fasta -db /var/lib/cwl/stgc3335c24-70d0-4b22-a029-e913bb4874d0/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2850/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 18:34:35,705] [INFO] Task succeeded: Blastn
[2023-03-16 18:34:35,707] [INFO] Selected 9 target genomes.
[2023-03-16 18:34:35,707] [INFO] Target genome list was writen to OceanDNA-a2850/target_genomes_gtdb.txt
[2023-03-16 18:34:35,711] [INFO] Task started: fastANI
[2023-03-16 18:34:35,711] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b30f257-ffdc-4678-9232-12cad272c9e4/OceanDNA-a2850.fa --refList OceanDNA-a2850/target_genomes_gtdb.txt --output OceanDNA-a2850/fastani_result_gtdb.tsv --threads 1
[2023-03-16 18:34:38,735] [INFO] Task succeeded: fastANI
[2023-03-16 18:34:38,741] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-16 18:34:38,741] [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_002719815.1	s__MGIIa-L2 sp002719815	99.626	425	569	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012270265.1	s__MGIIa-L2 sp012270265	79.7082	233	569	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018623995.1	s__MGIIa-L2 sp018623995	79.6057	251	569	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002499195.1	s__MGIIa-L2 sp002499195	79.4883	320	569	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	99.80	99.66	0.93	0.91	5	-
GCA_002706065.1	s__MGIIa-L2 sp002706065	78.8662	286	569	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002722615.1	s__MGIIa-L2 sp002722615	78.81	272	569	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	97.14	95.81	0.83	0.81	4	-
GCA_018645535.1	s__MGIIa-L2 sp018645535	77.1144	87	569	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602665.1	s__MGIIa-L2 sp003602665	76.9876	129	569	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L2	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-16 18:34:38,742] [INFO] GTDB search result was written to OceanDNA-a2850/result_gtdb.tsv
[2023-03-16 18:34:38,745] [INFO] ===== GTDB Search completed =====
[2023-03-16 18:34:38,747] [INFO] DFAST_QC result json was written to OceanDNA-a2850/dqc_result.json
[2023-03-16 18:34:38,747] [INFO] DFAST_QC completed!
[2023-03-16 18:34:38,747] [INFO] Total running time: 0h1m13s