[2023-03-18 20:55:47,277] [INFO] DFAST_QC pipeline started.
[2023-03-18 20:55:47,277] [INFO] DFAST_QC version: 0.5.7
[2023-03-18 20:55:47,278] [INFO] DQC Reference Directory: /var/lib/cwl/stg82039c18-36dd-42c1-88e4-cbff2e6f621c/dqc_reference
[2023-03-18 20:55:48,401] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-18 20:55:48,401] [INFO] Task started: Prodigal
[2023-03-18 20:55:48,401] [INFO] Running command: cat /var/lib/cwl/stg7e485ac7-0e67-4c1b-acee-5a0ebfc9468b/OceanDNA-b21158.fa | prodigal -d OceanDNA-b21158/cds.fna -a OceanDNA-b21158/protein.faa -g 11 -q > /dev/null
[2023-03-18 20:55:57,901] [INFO] Task succeeded: Prodigal
[2023-03-18 20:55:57,901] [INFO] Task started: HMMsearch
[2023-03-18 20:55:57,901] [INFO] Running command: hmmsearch --tblout OceanDNA-b21158/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg82039c18-36dd-42c1-88e4-cbff2e6f621c/dqc_reference/reference_markers.hmm OceanDNA-b21158/protein.faa > /dev/null
[2023-03-18 20:55:58,096] [INFO] Task succeeded: HMMsearch
[2023-03-18 20:55:58,097] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7e485ac7-0e67-4c1b-acee-5a0ebfc9468b/OceanDNA-b21158.fa]
[2023-03-18 20:55:58,112] [INFO] Query marker FASTA was written to OceanDNA-b21158/markers.fasta
[2023-03-18 20:55:58,113] [INFO] Task started: Blastn
[2023-03-18 20:55:58,113] [INFO] Running command: blastn -query OceanDNA-b21158/markers.fasta -db /var/lib/cwl/stg82039c18-36dd-42c1-88e4-cbff2e6f621c/dqc_reference/reference_markers.fasta -out OceanDNA-b21158/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:55:58,643] [INFO] Task succeeded: Blastn
[2023-03-18 20:55:58,644] [INFO] Selected 26 target genomes.
[2023-03-18 20:55:58,645] [INFO] Target genome list was writen to OceanDNA-b21158/target_genomes.txt
[2023-03-18 20:55:58,658] [INFO] Task started: fastANI
[2023-03-18 20:55:58,658] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e485ac7-0e67-4c1b-acee-5a0ebfc9468b/OceanDNA-b21158.fa --refList OceanDNA-b21158/target_genomes.txt --output OceanDNA-b21158/fastani_result.tsv --threads 1
[2023-03-18 20:56:12,017] [INFO] Task succeeded: fastANI
[2023-03-18 20:56:12,018] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg82039c18-36dd-42c1-88e4-cbff2e6f621c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-18 20:56:12,018] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg82039c18-36dd-42c1-88e4-cbff2e6f621c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-18 20:56:12,018] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-18 20:56:12,018] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-18 20:56:12,018] [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 20:56:12,018] [INFO] DFAST Taxonomy check result was written to OceanDNA-b21158/tc_result.tsv
[2023-03-18 20:56:12,018] [INFO] ===== Taxonomy check completed =====
[2023-03-18 20:56:12,018] [INFO] ===== Start completeness check using CheckM =====
[2023-03-18 20:56:12,018] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg82039c18-36dd-42c1-88e4-cbff2e6f621c/dqc_reference/checkm_data
[2023-03-18 20:56:12,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-18 20:56:12,024] [INFO] Task started: CheckM
[2023-03-18 20:56:12,024] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b21158/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b21158/checkm_input OceanDNA-b21158/checkm_result
[2023-03-18 20:56:40,692] [INFO] Task succeeded: CheckM
[2023-03-18 20:56:40,693] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 50.29%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-18 20:56:40,694] [INFO] ===== Completeness check finished =====
[2023-03-18 20:56:40,695] [INFO] ===== Start GTDB Search =====
[2023-03-18 20:56:40,695] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b21158/markers.fasta)
[2023-03-18 20:56:40,695] [INFO] Task started: Blastn
[2023-03-18 20:56:40,695] [INFO] Running command: blastn -query OceanDNA-b21158/markers.fasta -db /var/lib/cwl/stg82039c18-36dd-42c1-88e4-cbff2e6f621c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b21158/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-18 20:56:41,531] [INFO] Task succeeded: Blastn
[2023-03-18 20:56:41,532] [INFO] Selected 13 target genomes.
[2023-03-18 20:56:41,532] [INFO] Target genome list was writen to OceanDNA-b21158/target_genomes_gtdb.txt
[2023-03-18 20:56:41,613] [INFO] Task started: fastANI
[2023-03-18 20:56:41,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg7e485ac7-0e67-4c1b-acee-5a0ebfc9468b/OceanDNA-b21158.fa --refList OceanDNA-b21158/target_genomes_gtdb.txt --output OceanDNA-b21158/fastani_result_gtdb.tsv --threads 1
[2023-03-18 20:56:47,656] [INFO] Task succeeded: fastANI
[2023-03-18 20:56:47,662] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-18 20:56:47,662] [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_905612265.1	s__LS-NOB sp905612265	81.7902	134	561	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014382285.1	s__LS-NOB sp014382285	80.7175	341	561	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.85	99.85	0.92	0.92	2	-
GCA_001542995.1	s__LS-NOB sp001542995	79.3622	286	561	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002786505.1	s__LS-NOB sp002786505	78.6346	243	561	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018653085.1	s__LS-NOB sp018653085	78.0049	258	561	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.81	99.70	0.96	0.92	14	-
GCA_009873635.1	s__LS-NOB sp009873635	77.9171	204	561	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	99.03	98.80	0.95	0.93	3	-
GCA_002705185.1	s__LS-NOB sp002705185	77.7053	152	561	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003545625.1	s__LS-NOB sp003545625	77.4495	162	561	d__Bacteria;p__Nitrospinota;c__Nitrospinia;o__Nitrospinales;f__Nitrospinaceae;g__LS-NOB	95.0	98.65	98.65	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2023-03-18 20:56:47,662] [INFO] GTDB search result was written to OceanDNA-b21158/result_gtdb.tsv
[2023-03-18 20:56:47,662] [INFO] ===== GTDB Search completed =====
[2023-03-18 20:56:47,663] [INFO] DFAST_QC result json was written to OceanDNA-b21158/dqc_result.json
[2023-03-18 20:56:47,663] [INFO] DFAST_QC completed!
[2023-03-18 20:56:47,663] [INFO] Total running time: 0h1m0s