[2023-03-18 06:37:01,365] [INFO] DFAST_QC pipeline started.
[2023-03-18 06:37:01,365] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 06:37:01,365] [INFO] DQC Reference Directory: /var/lib/cwl/stge609728d-0cbf-40d0-9a53-7fb63b8a72e5/dqc_reference
[2023-03-18 06:37:02,499] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 06:37:02,500] [INFO] Task started: Prodigal
[2023-03-18 06:37:02,500] [INFO] Running command: cat /var/lib/cwl/stg2e9eb589-62b4-4b43-ad45-59ffda8a9035/OceanDNA-a2490.fa | prodigal -d OceanDNA-a2490/cds.fna -a OceanDNA-a2490/protein.faa -g 11 -q > /dev/null
[2023-03-18 06:37:13,217] [INFO] Task succeeded: Prodigal
[2023-03-18 06:37:13,217] [INFO] Task started: HMMsearch
[2023-03-18 06:37:13,217] [INFO] Running command: hmmsearch --tblout OceanDNA-a2490/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge609728d-0cbf-40d0-9a53-7fb63b8a72e5/dqc_reference/reference_markers.hmm OceanDNA-a2490/protein.faa > /dev/null
[2023-03-18 06:37:13,359] [INFO] Task succeeded: HMMsearch
[2023-03-18 06:37:13,360] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2e9eb589-62b4-4b43-ad45-59ffda8a9035/OceanDNA-a2490.fa]
[2023-03-18 06:37:13,373] [INFO] Query marker FASTA was written to OceanDNA-a2490/markers.fasta
[2023-03-18 06:37:13,374] [INFO] Task started: Blastn
[2023-03-18 06:37:13,374] [INFO] Running command: blastn -query OceanDNA-a2490/markers.fasta -db /var/lib/cwl/stge609728d-0cbf-40d0-9a53-7fb63b8a72e5/dqc_reference/reference_markers.fasta -out OceanDNA-a2490/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:37:13,806] [INFO] Task succeeded: Blastn
[2023-03-18 06:37:13,807] [INFO] Selected 3 target genomes.
[2023-03-18 06:37:13,807] [INFO] Target genome list was writen to OceanDNA-a2490/target_genomes.txt
[2023-03-18 06:37:13,808] [INFO] Task started: fastANI
[2023-03-18 06:37:13,809] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e9eb589-62b4-4b43-ad45-59ffda8a9035/OceanDNA-a2490.fa --refList OceanDNA-a2490/target_genomes.txt --output OceanDNA-a2490/fastani_result.tsv --threads 1
[2023-03-18 06:37:15,916] [INFO] Task succeeded: fastANI
[2023-03-18 06:37:15,917] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge609728d-0cbf-40d0-9a53-7fb63b8a72e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 06:37:15,917] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge609728d-0cbf-40d0-9a53-7fb63b8a72e5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 06:37:15,917] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 06:37:15,917] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 06:37:15,917] [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 06:37:15,917] [INFO] DFAST Taxonomy check result was written to OceanDNA-a2490/tc_result.tsv
[2023-03-18 06:37:15,917] [INFO] ===== Taxonomy check completed =====
[2023-03-18 06:37:15,918] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 06:37:15,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge609728d-0cbf-40d0-9a53-7fb63b8a72e5/dqc_reference/checkm_data
[2023-03-18 06:37:15,921] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 06:37:15,980] [INFO] Task started: CheckM
[2023-03-18 06:37:15,980] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-a2490/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-a2490/checkm_input OceanDNA-a2490/checkm_result
[2023-03-18 06:37:48,057] [INFO] Task succeeded: CheckM
[2023-03-18 06:37:48,058] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.07%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 06:37:48,060] [INFO] ===== Completeness check finished =====
[2023-03-18 06:37:48,060] [INFO] ===== Start GTDB Search =====
[2023-03-18 06:37:48,060] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-a2490/markers.fasta)
[2023-03-18 06:37:48,060] [INFO] Task started: Blastn
[2023-03-18 06:37:48,060] [INFO] Running command: blastn -query OceanDNA-a2490/markers.fasta -db /var/lib/cwl/stge609728d-0cbf-40d0-9a53-7fb63b8a72e5/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-a2490/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 06:37:48,490] [INFO] Task succeeded: Blastn
[2023-03-18 06:37:48,491] [INFO] Selected 10 target genomes.
[2023-03-18 06:37:48,491] [INFO] Target genome list was writen to OceanDNA-a2490/target_genomes_gtdb.txt
[2023-03-18 06:37:48,605] [INFO] Task started: fastANI
[2023-03-18 06:37:48,606] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e9eb589-62b4-4b43-ad45-59ffda8a9035/OceanDNA-a2490.fa --refList OceanDNA-a2490/target_genomes_gtdb.txt --output OceanDNA-a2490/fastani_result_gtdb.tsv --threads 1
[2023-03-18 06:37:52,223] [INFO] Task succeeded: fastANI
[2023-03-18 06:37:52,230] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-03-18 06:37:52,230] [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_002170315.2	s__MGIIa-L1 sp002170315	98.6501	490	567	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002499705.1	s__MGIIa-L1 sp002499705	84.2895	443	567	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_902520595.1	s__MGIIa-L1 sp902520595	83.1808	322	567	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_009937025.1	s__MGIIa-L1 sp009937025	79.9928	291	567	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_018662825.1	s__MGIIa-L1 sp018662825	79.4289	286	567	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	99.67	99.65	0.92	0.89	8	-
GCA_905182635.1	s__MGIIa-L1 sp905182635	78.9255	194	567	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_905182715.1	s__MGIIa-L1 sp905182715	78.7825	257	567	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_003602605.1	s__MGIIa-L1 sp003602605	78.1322	188	567	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_018691345.1	s__MGIIa-L1 sp018691345	78.0382	177	567	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_002687075.1	s__MGIIa-L1 sp002687075	78.0367	180	567	d__Archaea;p__Thermoplasmatota;c__Poseidoniia;o__Poseidoniales;f__Poseidoniaceae;g__MGIIa-L1	95.0	96.38	95.66	0.88	0.80	4	-
--------------------------------------------------------------------------------
[2023-03-18 06:37:52,230] [INFO] GTDB search result was written to OceanDNA-a2490/result_gtdb.tsv
[2023-03-18 06:37:52,230] [INFO] ===== GTDB Search completed =====
[2023-03-18 06:37:52,231] [INFO] DFAST_QC result json was written to OceanDNA-a2490/dqc_result.json
[2023-03-18 06:37:52,231] [INFO] DFAST_QC completed!
[2023-03-18 06:37:52,231] [INFO] Total running time: 0h0m51s