[2023-03-16 19:28:28,655] [INFO] DFAST_QC pipeline started.
[2023-03-16 19:28:28,655] [INFO] DFAST_QC version: 0.5.7
[2023-03-16 19:28:28,655] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2e23934-440a-42ae-8e58-3f71121aaa3c/dqc_reference
[2023-03-16 19:28:29,776] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-16 19:28:29,777] [INFO] Task started: Prodigal
[2023-03-16 19:28:29,777] [INFO] Running command: cat /var/lib/cwl/stg5d8da601-c137-4354-a2ee-d4ae28d5d3bf/OceanDNA-b30787.fa | prodigal -d OceanDNA-b30787/cds.fna -a OceanDNA-b30787/protein.faa -g 11 -q > /dev/null
[2023-03-16 19:28:35,879] [INFO] Task succeeded: Prodigal
[2023-03-16 19:28:35,880] [INFO] Task started: HMMsearch
[2023-03-16 19:28:35,880] [INFO] Running command: hmmsearch --tblout OceanDNA-b30787/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2e23934-440a-42ae-8e58-3f71121aaa3c/dqc_reference/reference_markers.hmm OceanDNA-b30787/protein.faa > /dev/null
[2023-03-16 19:28:36,128] [INFO] Task succeeded: HMMsearch
[2023-03-16 19:28:36,129] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5d8da601-c137-4354-a2ee-d4ae28d5d3bf/OceanDNA-b30787.fa]
[2023-03-16 19:28:36,144] [INFO] Query marker FASTA was written to OceanDNA-b30787/markers.fasta
[2023-03-16 19:28:36,150] [INFO] Task started: Blastn
[2023-03-16 19:28:36,150] [INFO] Running command: blastn -query OceanDNA-b30787/markers.fasta -db /var/lib/cwl/stgc2e23934-440a-42ae-8e58-3f71121aaa3c/dqc_reference/reference_markers.fasta -out OceanDNA-b30787/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:28:37,697] [INFO] Task succeeded: Blastn
[2023-03-16 19:28:37,698] [INFO] Selected 21 target genomes.
[2023-03-16 19:28:37,698] [INFO] Target genome list was writen to OceanDNA-b30787/target_genomes.txt
[2023-03-16 19:28:37,706] [INFO] Task started: fastANI
[2023-03-16 19:28:37,706] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d8da601-c137-4354-a2ee-d4ae28d5d3bf/OceanDNA-b30787.fa --refList OceanDNA-b30787/target_genomes.txt --output OceanDNA-b30787/fastani_result.tsv --threads 1
[2023-03-16 19:29:01,683] [INFO] Task succeeded: fastANI
[2023-03-16 19:29:01,683] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2e23934-440a-42ae-8e58-3f71121aaa3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-16 19:29:01,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2e23934-440a-42ae-8e58-3f71121aaa3c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-16 19:29:01,684] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-16 19:29:01,684] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-16 19:29:01,684] [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
--------------------------------------------------------------------------------
[2023-03-16 19:29:01,685] [INFO] DFAST Taxonomy check result was written to OceanDNA-b30787/tc_result.tsv
[2023-03-16 19:29:01,685] [INFO] ===== Taxonomy check completed =====
[2023-03-16 19:29:01,685] [INFO] ===== Start completeness check using CheckM =====
[2023-03-16 19:29:01,685] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2e23934-440a-42ae-8e58-3f71121aaa3c/dqc_reference/checkm_data
[2023-03-16 19:29:01,742] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-16 19:29:01,875] [INFO] Task started: CheckM
[2023-03-16 19:29:01,875] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b30787/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b30787/checkm_input OceanDNA-b30787/checkm_result
[2023-03-16 19:29:29,688] [INFO] Task succeeded: CheckM
[2023-03-16 19:29:29,688] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 41.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-16 19:29:29,691] [INFO] ===== Completeness check finished =====
[2023-03-16 19:29:29,691] [INFO] ===== Start GTDB Search =====
[2023-03-16 19:29:29,692] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b30787/markers.fasta)
[2023-03-16 19:29:29,693] [INFO] Task started: Blastn
[2023-03-16 19:29:29,693] [INFO] Running command: blastn -query OceanDNA-b30787/markers.fasta -db /var/lib/cwl/stgc2e23934-440a-42ae-8e58-3f71121aaa3c/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b30787/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-16 19:29:31,537] [INFO] Task succeeded: Blastn
[2023-03-16 19:29:31,539] [INFO] Selected 9 target genomes.
[2023-03-16 19:29:31,539] [INFO] Target genome list was writen to OceanDNA-b30787/target_genomes_gtdb.txt
[2023-03-16 19:29:31,548] [INFO] Task started: fastANI
[2023-03-16 19:29:31,548] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d8da601-c137-4354-a2ee-d4ae28d5d3bf/OceanDNA-b30787.fa --refList OceanDNA-b30787/target_genomes_gtdb.txt --output OceanDNA-b30787/fastani_result_gtdb.tsv --threads 1
[2023-03-16 19:29:38,634] [INFO] Task succeeded: fastANI
[2023-03-16 19:29:38,639] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-16 19:29:38,639] [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_002938315.1	s__Casp-alpha2 sp002938315	79.5497	113	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.33	99.24	0.87	0.79	4	-
GCA_014382345.1	s__Casp-alpha2 sp014382345	78.6831	84	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.86	99.86	0.92	0.92	2	-
GCA_016763915.1	s__Casp-alpha2 sp016763915	77.8719	63	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002686255.1	s__Casp-alpha2 sp002686255	77.8575	70	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	99.76	99.74	0.90	0.88	3	-
GCA_013203955.1	s__Casp-alpha2 sp013203955	77.7921	79	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204265.1	s__Casp-alpha2 sp013204265	77.7123	72	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001510075.1	s__Casp-alpha2 sp001510075	77.6667	54	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002938075.1	s__Casp-alpha2 sp002938075	77.5645	62	208	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodospirillales;f__Casp-alpha2;g__Casp-alpha2	95.0	98.70	98.63	0.78	0.77	3	-
--------------------------------------------------------------------------------
[2023-03-16 19:29:38,640] [INFO] GTDB search result was written to OceanDNA-b30787/result_gtdb.tsv
[2023-03-16 19:29:38,640] [INFO] ===== GTDB Search completed =====
[2023-03-16 19:29:38,641] [INFO] DFAST_QC result json was written to OceanDNA-b30787/dqc_result.json
[2023-03-16 19:29:38,642] [INFO] DFAST_QC completed!
[2023-03-16 19:29:38,642] [INFO] Total running time: 0h1m10s