[2023-03-17 10:35:02,807] [INFO] DFAST_QC pipeline started.
[2023-03-17 10:35:02,807] [INFO] DFAST_QC version: 0.5.7
[2023-03-17 10:35:02,807] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf938e30-fd86-4def-a5b3-fedae3f05911/dqc_reference
[2023-03-17 10:35:04,554] [INFO] ===== Start taxonomy check using ANI =====
[2023-03-17 10:35:04,555] [INFO] Task started: Prodigal
[2023-03-17 10:35:04,555] [INFO] Running command: cat /var/lib/cwl/stg1ceec2c3-29b5-4d85-85b3-c9d75eb18d34/OceanDNA-b3603.fa | prodigal -d OceanDNA-b3603/cds.fna -a OceanDNA-b3603/protein.faa -g 11 -q > /dev/null
[2023-03-17 10:35:12,959] [INFO] Task succeeded: Prodigal
[2023-03-17 10:35:12,959] [INFO] Task started: HMMsearch
[2023-03-17 10:35:12,959] [INFO] Running command: hmmsearch --tblout OceanDNA-b3603/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf938e30-fd86-4def-a5b3-fedae3f05911/dqc_reference/reference_markers.hmm OceanDNA-b3603/protein.faa > /dev/null
[2023-03-17 10:35:13,110] [INFO] Task succeeded: HMMsearch
[2023-03-17 10:35:13,110] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg1ceec2c3-29b5-4d85-85b3-c9d75eb18d34/OceanDNA-b3603.fa]
[2023-03-17 10:35:13,123] [INFO] Query marker FASTA was written to OceanDNA-b3603/markers.fasta
[2023-03-17 10:35:13,124] [INFO] Task started: Blastn
[2023-03-17 10:35:13,124] [INFO] Running command: blastn -query OceanDNA-b3603/markers.fasta -db /var/lib/cwl/stgaf938e30-fd86-4def-a5b3-fedae3f05911/dqc_reference/reference_markers.fasta -out OceanDNA-b3603/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:35:13,631] [INFO] Task succeeded: Blastn
[2023-03-17 10:35:13,632] [INFO] Selected 22 target genomes.
[2023-03-17 10:35:13,632] [INFO] Target genome list was writen to OceanDNA-b3603/target_genomes.txt
[2023-03-17 10:35:13,645] [INFO] Task started: fastANI
[2023-03-17 10:35:13,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ceec2c3-29b5-4d85-85b3-c9d75eb18d34/OceanDNA-b3603.fa --refList OceanDNA-b3603/target_genomes.txt --output OceanDNA-b3603/fastani_result.tsv --threads 1
[2023-03-17 10:35:26,333] [INFO] Task succeeded: fastANI
[2023-03-17 10:35:26,333] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf938e30-fd86-4def-a5b3-fedae3f05911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-03-17 10:35:26,333] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf938e30-fd86-4def-a5b3-fedae3f05911/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-03-17 10:35:26,334] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-03-17 10:35:26,334] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-03-17 10:35:26,334] [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
--------------------------------------------------------------------------------
[2023-03-17 10:35:26,334] [INFO] DFAST Taxonomy check result was written to OceanDNA-b3603/tc_result.tsv
[2023-03-17 10:35:26,334] [INFO] ===== Taxonomy check completed =====
[2023-03-17 10:35:26,335] [INFO] ===== Start completeness check using CheckM =====
[2023-03-17 10:35:26,335] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf938e30-fd86-4def-a5b3-fedae3f05911/dqc_reference/checkm_data
[2023-03-17 10:35:26,338] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-03-17 10:35:26,343] [INFO] Task started: CheckM
[2023-03-17 10:35:26,343] [INFO] Running command: checkm taxonomy_wf --tab_table -f OceanDNA-b3603/cc_result.tsv -t 1 life "Prokaryote" OceanDNA-b3603/checkm_input OceanDNA-b3603/checkm_result
[2023-03-17 10:35:52,634] [INFO] Task succeeded: CheckM
[2023-03-17 10:35:52,635] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.77%
Contamintation: 2.55%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-03-17 10:35:52,637] [INFO] ===== Completeness check finished =====
[2023-03-17 10:35:52,637] [INFO] ===== Start GTDB Search =====
[2023-03-17 10:35:52,637] [INFO] Query marker FASTA already exists. Will reuse it. (OceanDNA-b3603/markers.fasta)
[2023-03-17 10:35:52,638] [INFO] Task started: Blastn
[2023-03-17 10:35:52,638] [INFO] Running command: blastn -query OceanDNA-b3603/markers.fasta -db /var/lib/cwl/stgaf938e30-fd86-4def-a5b3-fedae3f05911/dqc_reference/reference_markers_gtdb.fasta -out OceanDNA-b3603/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-03-17 10:35:53,342] [INFO] Task succeeded: Blastn
[2023-03-17 10:35:53,343] [INFO] Selected 7 target genomes.
[2023-03-17 10:35:53,343] [INFO] Target genome list was writen to OceanDNA-b3603/target_genomes_gtdb.txt
[2023-03-17 10:35:53,543] [INFO] Task started: fastANI
[2023-03-17 10:35:53,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg1ceec2c3-29b5-4d85-85b3-c9d75eb18d34/OceanDNA-b3603.fa --refList OceanDNA-b3603/target_genomes_gtdb.txt --output OceanDNA-b3603/fastani_result_gtdb.tsv --threads 1
[2023-03-17 10:35:56,107] [INFO] Task succeeded: fastANI
[2023-03-17 10:35:56,112] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-03-17 10:35:56,112] [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_005800655.1	s__Sediminibacterium sp005800655	93.254	252	303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903953815.1	s__Sediminibacterium sp903953815	92.8938	267	303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	99.40	99.39	0.85	0.84	4	-
GCA_003509845.1	s__Sediminibacterium sp003509845	92.7896	214	303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009920495.1	s__Sediminibacterium sp009920495	90.8521	236	303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009693715.1	s__Sediminibacterium sp009693715	90.5091	239	303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903910765.1	s__Sediminibacterium sp903910765	89.1862	238	303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903824725.1	s__Sediminibacterium sp903824725	80.7319	208	303	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Chitinophagaceae;g__Sediminibacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-03-17 10:35:56,112] [INFO] GTDB search result was written to OceanDNA-b3603/result_gtdb.tsv
[2023-03-17 10:35:56,113] [INFO] ===== GTDB Search completed =====
[2023-03-17 10:35:56,113] [INFO] DFAST_QC result json was written to OceanDNA-b3603/dqc_result.json
[2023-03-17 10:35:56,113] [INFO] DFAST_QC completed!
[2023-03-17 10:35:56,113] [INFO] Total running time: 0h0m53s