[2023-03-19 02:10:16,859] [INFO] DFAST_QC pipeline started.
[2023-03-19 02:10:16,859] [INFO] DFAST_QC version: 0.5.7
[2023-03-19 02:10:16,859] [INFO] DQC Reference Directory: /var/lib/cwl/stg918ffb09-cfe5-453a-9604-ec4617ce32a6/dqc_reference
[2023-03-19 02:10:18,813] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-19 02:10:18,814] [INFO] Task started: Prodigal
[2023-03-19 02:10:18,814] [INFO] Running command: cat /var/lib/cwl/stg60ccff72-6e79-4ff6-b544-4e61c13d5dc4/OceanDNA-a2216.fa | prodigal -d OceanDNA-a2216/cds.fna -a OceanDNA-a2216/protein.faa -g 11 -q > /dev/null
[2023-03-19 02:10:25,927] [INFO] Task succeeded: Prodigal
[2023-03-19 02:10:25,928] [INFO] Task started: HMMsearch
[2023-03-19 02:10:25,928] [INFO] Running command: hmmsearch --tblout OceanDNA-a2216/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg918ffb09-cfe5-453a-9604-ec4617ce32a6/dqc_reference/reference_markers.hmm OceanDNA-a2216/protein.faa > /dev/null
[2023-03-19 02:10:26,074] [INFO] Task succeeded: HMMsearch
[2023-03-19 02:10:26,075] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg60ccff72-6e79-4ff6-b544-4e61c13d5dc4/OceanDNA-a2216.fa]
[2023-03-19 02:10:26,086] [INFO] Query marker FASTA was written to OceanDNA-a2216/markers.fasta
[2023-03-19 02:10:26,087] [INFO] Task started: Blastn
[2023-03-19 02:10:26,087] [INFO] Running command: blastn -query OceanDNA-a2216/markers.fasta -db /var/lib/cwl/stg918ffb09-cfe5-453a-9604-ec4617ce32a6/dqc_reference/reference_markers.fasta -out OceanDNA-a2216/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:10:26,546] [INFO] Task succeeded: Blastn
[2023-03-19 02:10:26,547] [INFO] Selected 4 target genomes.
[2023-03-19 02:10:26,547] [INFO] Target genome list was writen to OceanDNA-a2216/target_genomes.txt
[2023-03-19 02:10:26,550] [INFO] Task started: fastANI
[2023-03-19 02:10:26,550] [INFO] Running command: fastANI --query /var/lib/cwl/stg60ccff72-6e79-4ff6-b544-4e61c13d5dc4/OceanDNA-a2216.fa --refList OceanDNA-a2216/target_genomes.txt --output OceanDNA-a2216/fastani_result.tsv --threads 1
[2023-03-19 02:10:27,964] [INFO] Task succeeded: fastANI
[2023-03-19 02:10:27,964] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg918ffb09-cfe5-453a-9604-ec4617ce32a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-19 02:10:27,964] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg918ffb09-cfe5-453a-9604-ec4617ce32a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-19 02:10:27,964] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-19 02:10:27,964] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-19 02:10:27,964] [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
--------------------------------------------------------------------------------
[2023-03-19 02:10:27,965] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2216/tc_result.tsv
[2023-03-19 02:10:27,965] [INFO] ===== Taxonomy check completed =====
[2023-03-19 02:10:27,965] [INFO] ===== Start completeness check using CheckM =====
[2023-03-19 02:10:27,965] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg918ffb09-cfe5-453a-9604-ec4617ce32a6/dqc_reference/checkm_data
[2023-03-19 02:10:27,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-19 02:10:28,013] [INFO] Task started: CheckM
[2023-03-19 02:10:28,013] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2216/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2216/checkm_input OceanDNA-a2216/checkm_result
[2023-03-19 02:10:52,960] [INFO] Task succeeded: CheckM
[2023-03-19 02:10:52,961] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.80%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-19 02:10:52,962] [INFO] ===== Completeness check finished =====
[2023-03-19 02:10:52,962] [INFO] ===== Start GTDB Search =====
[2023-03-19 02:10:52,963] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2216/markers.fasta)
[2023-03-19 02:10:52,963] [INFO] Task started: Blastn
[2023-03-19 02:10:52,963] [INFO] Running command: blastn -query OceanDNA-a2216/markers.fasta -db /var/lib/cwl/stg918ffb09-cfe5-453a-9604-ec4617ce32a6/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2216/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-19 02:10:53,510] [INFO] Task succeeded: Blastn
[2023-03-19 02:10:53,511] [INFO] Selected 12 target genomes.
[2023-03-19 02:10:53,511] [INFO] Target genome list was writen to OceanDNA-a2216/target_genomes_gtdb.txt
[2023-03-19 02:10:53,587] [INFO] Task started: fastANI
[2023-03-19 02:10:53,587] [INFO] Running command: fastANI --query /var/lib/cwl/stg60ccff72-6e79-4ff6-b544-4e61c13d5dc4/OceanDNA-a2216.fa --refList OceanDNA-a2216/target_genomes_gtdb.txt --output OceanDNA-a2216/fastani_result_gtdb.tsv --threads 1
[2023-03-19 02:10:57,439] [INFO] Task succeeded: fastANI
[2023-03-19 02:10:57,444] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-19 02:10:57,445] [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_013329255.1	s__MGIIa-L1 sp9513u	80.8108	173	303	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	100.00	100.00	0.97	0.97	2	-
GCA_905181785.1	s__MGIIa-L1 sp905181785	80.0948	161	303	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009887095.1	s__MGIIa-L1 sp009887095	78.7321	102	303	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182125.1	s__MGIIa-L1 sp905182125	78.7041	117	303	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000246735.1	s__MGIIa-L1 sp000246735	78.445	132	303	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.40	99.32	0.97	0.89	6	-
GCA_002495535.1	s__MGIIa-L1 sp002495535	78.1548	133	303	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013330285.1	s__MGIIa-L1 sp8160u	77.8485	90	303	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	97.88	96.83	0.79	0.69	4	-
--------------------------------------------------------------------------------
[2023-03-19 02:10:57,445] [INFO] GTDB search result was written to OceanDNA-a2216/result_gtdb.tsv
[2023-03-19 02:10:57,445] [INFO] ===== GTDB Search completed =====
[2023-03-19 02:10:57,448] [INFO] DFAST_QC result json was written to OceanDNA-a2216/dqc_result.json
[2023-03-19 02:10:57,449] [INFO] DFAST_QC completed!
[2023-03-19 02:10:57,449] [INFO] Total running time: 0h0m41s