[2023-03-18 22:44:57,810] [INFO] DFAST_QC pipeline started.
[2023-03-18 22:44:57,811] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 22:44:57,811] [INFO] DQC Reference Directory: /var/lib/cwl/stge8c21146-3e44-4914-bd3b-28691e43ba30/dqc_reference
[2023-03-18 22:44:58,938] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 22:44:58,938] [INFO] Task started: Prodigal
[2023-03-18 22:44:58,938] [INFO] Running command: cat /var/lib/cwl/stg2dd3b5c5-c5e3-4de5-a897-a07435974496/OceanDNA-a1855.fa | prodigal -d OceanDNA-a1855/cds.fna -a OceanDNA-a1855/protein.faa -g 11 -q > /dev/null
[2023-03-18 22:45:06,942] [INFO] Task succeeded: Prodigal
[2023-03-18 22:45:06,942] [INFO] Task started: HMMsearch
[2023-03-18 22:45:06,942] [INFO] Running command: hmmsearch --tblout OceanDNA-a1855/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge8c21146-3e44-4914-bd3b-28691e43ba30/dqc_reference/reference_markers.hmm OceanDNA-a1855/protein.faa > /dev/null
[2023-03-18 22:45:07,100] [INFO] Task succeeded: HMMsearch
[2023-03-18 22:45:07,100] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2dd3b5c5-c5e3-4de5-a897-a07435974496/OceanDNA-a1855.fa]
[2023-03-18 22:45:07,112] [INFO] Query marker FASTA was written to OceanDNA-a1855/markers.fasta
[2023-03-18 22:45:07,113] [INFO] Task started: Blastn
[2023-03-18 22:45:07,113] [INFO] Running command: blastn -query OceanDNA-a1855/markers.fasta -db /var/lib/cwl/stge8c21146-3e44-4914-bd3b-28691e43ba30/dqc_reference/reference_markers.fasta -out OceanDNA-a1855/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:45:07,536] [INFO] Task succeeded: Blastn
[2023-03-18 22:45:07,536] [INFO] Selected 6 target genomes.
[2023-03-18 22:45:07,536] [INFO] Target genome list was writen to OceanDNA-a1855/target_genomes.txt
[2023-03-18 22:45:07,540] [INFO] Task started: fastANI
[2023-03-18 22:45:07,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dd3b5c5-c5e3-4de5-a897-a07435974496/OceanDNA-a1855.fa --refList OceanDNA-a1855/target_genomes.txt --output OceanDNA-a1855/fastani_result.tsv --threads 1
[2023-03-18 22:45:09,718] [INFO] Task succeeded: fastANI
[2023-03-18 22:45:09,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge8c21146-3e44-4914-bd3b-28691e43ba30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 22:45:09,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge8c21146-3e44-4914-bd3b-28691e43ba30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 22:45:09,719] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 22:45:09,719] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 22:45:09,719] [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
--------------------------------------------------------------------------------
[2023-03-18 22:45:09,719] [INFO] DFAST Taxonomy check result was written to OceanDNA-a1855/tc_result.tsv
[2023-03-18 22:45:09,719] [INFO] ===== Taxonomy check completed =====
[2023-03-18 22:45:09,719] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 22:45:09,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge8c21146-3e44-4914-bd3b-28691e43ba30/dqc_reference/checkm_data
[2023-03-18 22:45:09,730] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 22:45:09,733] [INFO] Task started: CheckM
[2023-03-18 22:45:09,733] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a1855/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a1855/checkm_input OceanDNA-a1855/checkm_result
[2023-03-18 22:45:34,907] [INFO] Task succeeded: CheckM
[2023-03-18 22:45:34,907] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.80%
Contamintation: 9.38%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-03-18 22:45:34,909] [INFO] ===== Completeness check finished =====
[2023-03-18 22:45:34,909] [INFO] ===== Start GTDB Search =====
[2023-03-18 22:45:34,909] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a1855/markers.fasta)
[2023-03-18 22:45:34,910] [INFO] Task started: Blastn
[2023-03-18 22:45:34,910] [INFO] Running command: blastn -query OceanDNA-a1855/markers.fasta -db /var/lib/cwl/stge8c21146-3e44-4914-bd3b-28691e43ba30/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a1855/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 22:45:35,333] [INFO] Task succeeded: Blastn
[2023-03-18 22:45:35,334] [INFO] Selected 14 target genomes.
[2023-03-18 22:45:35,334] [INFO] Target genome list was writen to OceanDNA-a1855/target_genomes_gtdb.txt
[2023-03-18 22:45:35,354] [INFO] Task started: fastANI
[2023-03-18 22:45:35,354] [INFO] Running command: fastANI --query /var/lib/cwl/stg2dd3b5c5-c5e3-4de5-a897-a07435974496/OceanDNA-a1855.fa --refList OceanDNA-a1855/target_genomes_gtdb.txt --output OceanDNA-a1855/fastani_result_gtdb.tsv --threads 1
[2023-03-18 22:45:39,296] [INFO] Task succeeded: fastANI
[2023-03-18 22:45:39,303] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 22:45:39,303] [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_002506705.1	s__MGIIa-K1 sp002506705	81.7976	228	458	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011525095.1	s__MGIIa-K1 sp011525095	81.4275	267	458	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002727695.1	s__MGIIa-K1 sp002727695	78.4141	147	458	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002498185.1	s__MGIIa-K1 sp002498185	78.2221	157	458	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	99.51	99.39	0.80	0.77	3	-
GCA_902563095.1	s__MGIIa-K1 sp902563095	77.9858	118	458	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	98.06	97.94	0.61	0.59	4	-
GCA_002710205.1	s__MGIIa-K1 sp002710205	77.7667	132	458	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689565.1	s__MGIIa-K1 sp002689565	77.6304	99	458	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003602415.1	s__MGIIa-K1 sp003602415	77.2321	139	458	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	97.94	97.94	0.93	0.93	2	-
GCA_002701145.1	s__MGIIa-K1 sp002701145	76.6877	79	458	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002689345.1	s__MGIIa-K1 sp002689345	76.5942	96	458	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-K1	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-18 22:45:39,303] [INFO] GTDB search result was written to OceanDNA-a1855/result_gtdb.tsv
[2023-03-18 22:45:39,303] [INFO] ===== GTDB Search completed =====
[2023-03-18 22:45:39,304] [INFO] DFAST_QC result json was written to OceanDNA-a1855/dqc_result.json
[2023-03-18 22:45:39,304] [INFO] DFAST_QC completed!
[2023-03-18 22:45:39,304] [INFO] Total running time: 0h0m41s