[2023-06-13 10:10:45,782] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:10:45,786] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:10:45,787] [INFO] DQC Reference Directory: /var/lib/cwl/stg0691bea3-7d63-49f2-b93f-d997e6086c9f/dqc_reference
[2023-06-13 10:10:47,136] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:10:47,137] [INFO] Task started: Prodigal
[2023-06-13 10:10:47,137] [INFO] Running command: gunzip -c /var/lib/cwl/stg05776d2d-b982-4f75-8519-195e2ad46773/GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna.gz | prodigal -d GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/cds.fna -a GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:10:47,878] [INFO] Task succeeded: Prodigal
[2023-06-13 10:10:47,878] [INFO] Task started: HMMsearch
[2023-06-13 10:10:47,878] [INFO] Running command: hmmsearch --tblout GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0691bea3-7d63-49f2-b93f-d997e6086c9f/dqc_reference/reference_markers.hmm GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:10:47,989] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:10:47,990] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg05776d2d-b982-4f75-8519-195e2ad46773/GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna.gz]
[2023-06-13 10:10:48,003] [INFO] Query marker FASTA was written to GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/markers.fasta
[2023-06-13 10:10:48,003] [INFO] Task started: Blastn
[2023-06-13 10:10:48,004] [INFO] Running command: blastn -query GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0691bea3-7d63-49f2-b93f-d997e6086c9f/dqc_reference/reference_markers.fasta -out GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:10:48,615] [INFO] Task succeeded: Blastn
[2023-06-13 10:10:48,619] [INFO] Selected 12 target genomes.
[2023-06-13 10:10:48,619] [INFO] Target genome list was writen to GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/target_genomes.txt
[2023-06-13 10:10:48,623] [INFO] Task started: fastANI
[2023-06-13 10:10:48,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg05776d2d-b982-4f75-8519-195e2ad46773/GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna.gz --refList GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/target_genomes.txt --output GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:10:53,287] [INFO] Task succeeded: fastANI
[2023-06-13 10:10:53,287] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0691bea3-7d63-49f2-b93f-d997e6086c9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:10:53,288] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0691bea3-7d63-49f2-b93f-d997e6086c9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:10:53,290] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 10:10:53,290] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 10:10:53,290] [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
--------------------------------------------------------------------------------
[2023-06-13 10:10:53,293] [INFO] DFAST Taxonomy check result was written to GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/tc_result.tsv
[2023-06-13 10:10:53,294] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:10:53,294] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:10:53,294] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0691bea3-7d63-49f2-b93f-d997e6086c9f/dqc_reference/checkm_data
[2023-06-13 10:10:53,297] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:10:53,306] [INFO] Task started: CheckM
[2023-06-13 10:10:53,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/checkm_input GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/checkm_result
[2023-06-13 10:11:04,842] [INFO] Task succeeded: CheckM
[2023-06-13 10:11:04,843] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 10:11:04,857] [INFO] ===== Completeness check finished =====
[2023-06-13 10:11:04,858] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:11:04,858] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/markers.fasta)
[2023-06-13 10:11:04,858] [INFO] Task started: Blastn
[2023-06-13 10:11:04,858] [INFO] Running command: blastn -query GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0691bea3-7d63-49f2-b93f-d997e6086c9f/dqc_reference/reference_markers_gtdb.fasta -out GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:11:05,452] [INFO] Task succeeded: Blastn
[2023-06-13 10:11:05,455] [INFO] Selected 12 target genomes.
[2023-06-13 10:11:05,456] [INFO] Target genome list was writen to GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:11:05,457] [INFO] Task started: fastANI
[2023-06-13 10:11:05,457] [INFO] Running command: fastANI --query /var/lib/cwl/stg05776d2d-b982-4f75-8519-195e2ad46773/GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna.gz --refList GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/target_genomes_gtdb.txt --output GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:11:07,290] [INFO] Task succeeded: fastANI
[2023-06-13 10:11:07,299] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-13 10:11:07,299] [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_902599655.1	s__Marinisoma sp902599655	80.8568	67	140	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	97.53	97.28	0.66	0.66	3	-
GCA_902538565.1	s__Marinisoma sp902538565	80.4961	100	140	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.07	99.04	0.96	0.96	3	-
GCA_016777965.1	s__Marinisoma sp016777965	80.3349	82	140	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902578385.1	s__Marinisoma sp002710515	80.2854	84	140	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	97.88	96.56	0.86	0.83	7	-
GCA_000402655.1	s__Marinisoma sp000402655	80.1705	92	140	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.42	95.83	0.93	0.92	4	-
GCA_902576865.1	s__Marinisoma sp902576865	80.1678	71	140	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	96.64	96.64	0.80	0.80	2	-
GCA_902624275.1	s__Marinisoma sp902624275	79.3824	82	140	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000402815.1	s__Marinisoma atlanticum	79.2071	57	140	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	99.54	99.22	0.95	0.89	4	-
GCA_902629855.1	s__Marinisoma sp902629855	78.7638	73	140	d__Bacteria;p__Marinisomatota;c__Marinisomatia;o__Marinisomatales;f__Marinisomataceae;g__Marinisoma	95.0	98.59	98.03	0.85	0.83	5	-
--------------------------------------------------------------------------------
[2023-06-13 10:11:07,301] [INFO] GTDB search result was written to GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/result_gtdb.tsv
[2023-06-13 10:11:07,302] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:11:07,305] [INFO] DFAST_QC result json was written to GCA_938041145.1_S1_Bin_METABAT_26_1_genomic.fna/dqc_result.json
[2023-06-13 10:11:07,305] [INFO] DFAST_QC completed!
[2023-06-13 10:11:07,305] [INFO] Total running time: 0h0m22s