[2023-03-18 00:53:42,517] [INFO] DFAST_QC pipeline started.
[2023-03-18 00:53:42,523] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 00:53:42,523] [INFO] DQC Reference Directory: /var/lib/cwl/stg205c5f1b-98ba-4c78-9663-ead9117424db/dqc_reference
[2023-03-18 00:53:43,645] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 00:53:43,645] [INFO] Task started: Prodigal
[2023-03-18 00:53:43,645] [INFO] Running command: cat /var/lib/cwl/stgc9077df9-ce2e-4e6f-9a57-4d022ca89b24/OceanDNA-a4758.fa | prodigal -d OceanDNA-a4758/cds.fna -a OceanDNA-a4758/protein.faa -g 11 -q > /dev/null
[2023-03-18 00:53:51,550] [INFO] Task succeeded: Prodigal
[2023-03-18 00:53:51,550] [INFO] Task started: HMMsearch
[2023-03-18 00:53:51,550] [INFO] Running command: hmmsearch --tblout OceanDNA-a4758/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg205c5f1b-98ba-4c78-9663-ead9117424db/dqc_reference/reference_markers.hmm OceanDNA-a4758/protein.faa > /dev/null
[2023-03-18 00:53:51,699] [INFO] Task succeeded: HMMsearch
[2023-03-18 00:53:51,700] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgc9077df9-ce2e-4e6f-9a57-4d022ca89b24/OceanDNA-a4758.fa]
[2023-03-18 00:53:51,711] [INFO] Query marker FASTA was written to OceanDNA-a4758/markers.fasta
[2023-03-18 00:53:51,711] [INFO] Task started: Blastn
[2023-03-18 00:53:51,711] [INFO] Running command: blastn -query OceanDNA-a4758/markers.fasta -db /var/lib/cwl/stg205c5f1b-98ba-4c78-9663-ead9117424db/dqc_reference/reference_markers.fasta -out OceanDNA-a4758/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:53:52,137] [INFO] Task succeeded: Blastn
[2023-03-18 00:53:52,138] [INFO] Selected 0 target genomes.
[2023-03-18 00:53:52,138] [INFO] Target genome list was writen to OceanDNA-a4758/target_genomes.txt
[2023-03-18 00:53:52,138] [ERROR] File is empty. [OceanDNA-a4758/target_genomes.txt]
[2023-03-18 00:53:52,138] [ERROR] Task failed. No target genome found.
[2023-03-18 00:53:52,138] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 00:53:52,138] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg205c5f1b-98ba-4c78-9663-ead9117424db/dqc_reference/checkm_data
[2023-03-18 00:53:52,141] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 00:53:52,144] [INFO] Task started: CheckM
[2023-03-18 00:53:52,144] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a4758/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a4758/checkm_input OceanDNA-a4758/checkm_result
[2023-03-18 00:54:18,000] [INFO] Task succeeded: CheckM
[2023-03-18 00:54:18,001] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.78%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-03-18 00:54:18,033] [INFO] ===== Completeness check finished =====
[2023-03-18 00:54:18,033] [INFO] ===== Start GTDB Search =====
[2023-03-18 00:54:18,033] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a4758/markers.fasta)
[2023-03-18 00:54:18,035] [INFO] Task started: Blastn
[2023-03-18 00:54:18,035] [INFO] Running command: blastn -query OceanDNA-a4758/markers.fasta -db /var/lib/cwl/stg205c5f1b-98ba-4c78-9663-ead9117424db/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a4758/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 00:54:18,487] [INFO] Task succeeded: Blastn
[2023-03-18 00:54:18,491] [INFO] Selected 9 target genomes.
[2023-03-18 00:54:18,491] [INFO] Target genome list was writen to OceanDNA-a4758/target_genomes_gtdb.txt
[2023-03-18 00:54:18,500] [INFO] Task started: fastANI
[2023-03-18 00:54:18,500] [INFO] Running command: fastANI --query /var/lib/cwl/stgc9077df9-ce2e-4e6f-9a57-4d022ca89b24/OceanDNA-a4758.fa --refList OceanDNA-a4758/target_genomes_gtdb.txt --output OceanDNA-a4758/fastani_result_gtdb.tsv --threads 1
[2023-03-18 00:54:21,417] [INFO] Task succeeded: fastANI
[2023-03-18 00:54:21,422] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 00:54:21,422] [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_002701965.1	s__MGIIb-P sp002701965	90.2388	273	391	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-P	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002498455.1	s__MGIIb-P sp002498455	81.3077	287	391	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-P	95.0	98.13	97.46	0.87	0.81	6	-
GCA_002724815.1	s__MGIIb-P sp002724815	81.2077	282	391	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-P	95.0	96.66	96.66	0.89	0.89	2	-
GCA_002713555.1	s__Bythopirellula sp002713555	80.0678	77	391	d__Bacteria;p__Planctomycetota;c__Planctomycetia;o__Pirellulales;f__Lacipirellulaceae;g__Bythopirellula	95.0	99.19	98.89	0.81	0.78	3	-
GCA_002505685.1	s__MGIIb-P sp002505685	79.1041	188	391	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-P	95.0	99.68	99.68	0.73	0.73	2	-
GCA_002457195.1	s__MGIIb-P sp002457195	77.6597	86	391	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Thalassarchaeaceae;g__MGIIb-P	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 00:54:21,423] [INFO] GTDB search result was written to OceanDNA-a4758/result_gtdb.tsv
[2023-03-18 00:54:21,424] [INFO] ===== GTDB Search completed =====
[2023-03-18 00:54:21,426] [INFO] DFAST_QC result json was written to OceanDNA-a4758/dqc_result.json
[2023-03-18 00:54:21,426] [INFO] DFAST_QC completed!
[2023-03-18 00:54:21,426] [INFO] Total running time: 0h0m39s