[2023-03-15 14:38:44,427] [INFO] DFAST_QC pipeline started.
[2023-03-15 14:38:44,427] [INFO] DFAST_QC version: 0.5.7
[2023-03-15 14:38:44,427] [INFO] DQC Reference Directory: /var/lib/cwl/stg395ae8d7-fdd3-4e3b-abb6-6c6061f425ea/dqc_reference
[2023-03-15 14:38:45,537] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-15 14:38:45,537] [INFO] Task started: Prodigal
[2023-03-15 14:38:45,537] [INFO] Running command: cat /var/lib/cwl/stgd5a14ddd-27d7-444a-9532-ca67d4e10f8f/OceanDNA-a2908.fa | prodigal -d OceanDNA-a2908/cds.fna -a OceanDNA-a2908/protein.faa -g 11 -q > /dev/null
[2023-03-15 14:38:57,794] [INFO] Task succeeded: Prodigal
[2023-03-15 14:38:57,794] [INFO] Task started: HMMsearch
[2023-03-15 14:38:57,794] [INFO] Running command: hmmsearch --tblout OceanDNA-a2908/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg395ae8d7-fdd3-4e3b-abb6-6c6061f425ea/dqc_reference/reference_markers.hmm OceanDNA-a2908/protein.faa > /dev/null
[2023-03-15 14:38:57,965] [INFO] Task succeeded: HMMsearch
[2023-03-15 14:38:57,965] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd5a14ddd-27d7-444a-9532-ca67d4e10f8f/OceanDNA-a2908.fa]
[2023-03-15 14:38:57,977] [INFO] Query marker FASTA was written to OceanDNA-a2908/markers.fasta
[2023-03-15 14:38:57,979] [INFO] Task started: Blastn
[2023-03-15 14:38:57,979] [INFO] Running command: blastn -query OceanDNA-a2908/markers.fasta -db /var/lib/cwl/stg395ae8d7-fdd3-4e3b-abb6-6c6061f425ea/dqc_reference/reference_markers.fasta -out OceanDNA-a2908/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:38:58,426] [INFO] Task succeeded: Blastn
[2023-03-15 14:38:58,426] [INFO] Selected 5 target genomes.
[2023-03-15 14:38:58,427] [INFO] Target genome list was writen to OceanDNA-a2908/target_genomes.txt
[2023-03-15 14:38:58,430] [INFO] Task started: fastANI
[2023-03-15 14:38:58,430] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5a14ddd-27d7-444a-9532-ca67d4e10f8f/OceanDNA-a2908.fa --refList OceanDNA-a2908/target_genomes.txt --output OceanDNA-a2908/fastani_result.tsv --threads 1
[2023-03-15 14:39:03,714] [INFO] Task succeeded: fastANI
[2023-03-15 14:39:03,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg395ae8d7-fdd3-4e3b-abb6-6c6061f425ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-15 14:39:03,714] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg395ae8d7-fdd3-4e3b-abb6-6c6061f425ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-15 14:39:03,715] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-15 14:39:03,715] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-15 14:39:03,715] [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
--------------------------------------------------------------------------------
[2023-03-15 14:39:03,715] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2908/tc_result.tsv
[2023-03-15 14:39:03,715] [INFO] ===== Taxonomy check completed =====
[2023-03-15 14:39:03,715] [INFO] ===== Start completeness check using CheckM =====
[2023-03-15 14:39:03,715] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg395ae8d7-fdd3-4e3b-abb6-6c6061f425ea/dqc_reference/checkm_data
[2023-03-15 14:39:03,718] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-15 14:39:03,740] [INFO] Task started: CheckM
[2023-03-15 14:39:03,740] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2908/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2908/checkm_input OceanDNA-a2908/checkm_result
[2023-03-15 14:39:42,692] [INFO] Task succeeded: CheckM
[2023-03-15 14:39:42,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 89.76%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-15 14:39:42,718] [INFO] ===== Completeness check finished =====
[2023-03-15 14:39:42,719] [INFO] ===== Start GTDB Search =====
[2023-03-15 14:39:42,719] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2908/markers.fasta)
[2023-03-15 14:39:42,720] [INFO] Task started: Blastn
[2023-03-15 14:39:42,720] [INFO] Running command: blastn -query OceanDNA-a2908/markers.fasta -db /var/lib/cwl/stg395ae8d7-fdd3-4e3b-abb6-6c6061f425ea/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2908/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-15 14:39:43,160] [INFO] Task succeeded: Blastn
[2023-03-15 14:39:43,161] [INFO] Selected 8 target genomes.
[2023-03-15 14:39:43,161] [INFO] Target genome list was writen to OceanDNA-a2908/target_genomes_gtdb.txt
[2023-03-15 14:39:43,168] [INFO] Task started: fastANI
[2023-03-15 14:39:43,168] [INFO] Running command: fastANI --query /var/lib/cwl/stgd5a14ddd-27d7-444a-9532-ca67d4e10f8f/OceanDNA-a2908.fa --refList OceanDNA-a2908/target_genomes_gtdb.txt --output OceanDNA-a2908/fastani_result_gtdb.tsv --threads 1
[2023-03-15 14:39:45,927] [INFO] Task succeeded: fastANI
[2023-03-15 14:39:45,933] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-15 14:39:45,933] [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_002731395.1	s__MGIIa-L3 sp002731395	98.743	399	556	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L3	95.0	99.15	99.02	0.81	0.76	3	conclusive
GCA_002722135.1	s__MGIIa-L3 sp002722135	85.679	474	556	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L3	95.0	99.74	99.72	0.92	0.89	4	-
GCA_002694585.1	s__MGIIa-L3 sp002694585	84.9828	396	556	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002496845.1	s__MGIIa-L3 sp002496845	82.0896	355	556	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L3	95.0	99.68	99.68	0.95	0.95	2	-
GCA_003602635.1	s__MGIIa-L3 sp003602635	80.9076	308	556	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L3	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013330925.1	s__MGIIa-L3 sp11892u	80.6833	278	556	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L3	95.0	99.55	99.23	0.93	0.88	5	-
GCA_013330765.1	s__MGIIa-L3 sp12206u	80.1971	220	556	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L3	95.0	100.00	100.00	0.99	0.99	2	-
GCA_002694525.1	s__Poseidonia sp002694525	76.635	54	556	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__Poseidonia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-15 14:39:45,933] [INFO] GTDB search result was written to OceanDNA-a2908/result_gtdb.tsv
[2023-03-15 14:39:45,933] [INFO] ===== GTDB Search completed =====
[2023-03-15 14:39:45,934] [INFO] DFAST_QC result json was written to OceanDNA-a2908/dqc_result.json
[2023-03-15 14:39:45,934] [INFO] DFAST_QC completed!
[2023-03-15 14:39:45,934] [INFO] Total running time: 0h1m2s