[2023-06-05 18:02:55,301] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:02:55,303] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:02:55,303] [INFO] DQC Reference Directory: /var/lib/cwl/stg729214e1-8e8c-4cc2-a794-ee6f3d130324/dqc_reference
[2023-06-05 18:02:56,593] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:02:56,593] [INFO] Task started: Prodigal
[2023-06-05 18:02:56,594] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd178872-b9bd-42e7-9784-e5c9501d7bcc/GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna.gz | prodigal -d GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/cds.fna -a GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:03:02,983] [INFO] Task succeeded: Prodigal
[2023-06-05 18:03:02,983] [INFO] Task started: HMMsearch
[2023-06-05 18:03:02,983] [INFO] Running command: hmmsearch --tblout GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg729214e1-8e8c-4cc2-a794-ee6f3d130324/dqc_reference/reference_markers.hmm GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:03:03,141] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:03:03,142] [INFO] Found 6/6 markers.
[2023-06-05 18:03:03,182] [INFO] Query marker FASTA was written to GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/markers.fasta
[2023-06-05 18:03:03,182] [INFO] Task started: Blastn
[2023-06-05 18:03:03,182] [INFO] Running command: blastn -query GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stg729214e1-8e8c-4cc2-a794-ee6f3d130324/dqc_reference/reference_markers.fasta -out GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:03:03,745] [INFO] Task succeeded: Blastn
[2023-06-05 18:03:03,750] [INFO] Selected 15 target genomes.
[2023-06-05 18:03:03,750] [INFO] Target genome list was writen to GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/target_genomes.txt
[2023-06-05 18:03:03,760] [INFO] Task started: fastANI
[2023-06-05 18:03:03,760] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd178872-b9bd-42e7-9784-e5c9501d7bcc/GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna.gz --refList GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/target_genomes.txt --output GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:03:15,272] [INFO] Task succeeded: fastANI
[2023-06-05 18:03:15,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg729214e1-8e8c-4cc2-a794-ee6f3d130324/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:03:15,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg729214e1-8e8c-4cc2-a794-ee6f3d130324/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:03:15,274] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:03:15,274] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:03:15,274] [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
--------------------------------------------------------------------------------
[2023-06-05 18:03:15,276] [INFO] DFAST Taxonomy check result was written to GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/tc_result.tsv
[2023-06-05 18:03:15,276] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:03:15,276] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:03:15,276] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg729214e1-8e8c-4cc2-a794-ee6f3d130324/dqc_reference/checkm_data
[2023-06-05 18:03:15,279] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:03:15,307] [INFO] Task started: CheckM
[2023-06-05 18:03:15,307] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/checkm_input GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/checkm_result
[2023-06-05 18:03:33,936] [INFO] Task succeeded: CheckM
[2023-06-05 18:03:33,937] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 18:03:33,955] [INFO] ===== Completeness check finished =====
[2023-06-05 18:03:33,955] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:03:33,956] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/markers.fasta)
[2023-06-05 18:03:33,956] [INFO] Task started: Blastn
[2023-06-05 18:03:33,956] [INFO] Running command: blastn -query GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/markers.fasta -db /var/lib/cwl/stg729214e1-8e8c-4cc2-a794-ee6f3d130324/dqc_reference/reference_markers_gtdb.fasta -out GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:03:34,853] [INFO] Task succeeded: Blastn
[2023-06-05 18:03:34,857] [INFO] Selected 11 target genomes.
[2023-06-05 18:03:34,858] [INFO] Target genome list was writen to GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:03:34,943] [INFO] Task started: fastANI
[2023-06-05 18:03:34,943] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd178872-b9bd-42e7-9784-e5c9501d7bcc/GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna.gz --refList GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/target_genomes_gtdb.txt --output GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:03:37,439] [INFO] Task succeeded: fastANI
[2023-06-05 18:03:37,446] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:03:37,447] [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_003476885.1	s__Limnocylindrus sp003476885	95.3573	211	345	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_903937225.1	s__Limnocylindrus sp903937225	93.2389	200	345	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003670475.1	s__Limnocylindrus sp003670475	82.8351	193	345	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	98.28	98.28	0.88	0.88	2	-
GCA_903944295.1	s__Limnocylindrus sp903944295	82.6687	192	345	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	99.38	99.18	0.85	0.81	11	-
GCA_903847005.1	s__Limnocylindrus sp903847005	81.4505	155	345	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003670745.1	s__Limnocylindrus sp003670745	78.8229	121	345	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463555.1	s__Limnocylindrus sp016463555	78.7212	99	345	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	98.54	98.47	0.78	0.78	3	-
GCA_903820655.1	s__Limnocylindrus sp903820655	78.4535	77	345	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903864185.1	s__Limnocylindrus sp903864185	78.2176	99	345	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	98.90	97.48	0.92	0.89	6	-
GCA_903851225.1	s__Limnocylindrus sp903851225	77.9708	85	345	d__Bacteria;p__Chloroflexota;c__Limnocylindria;o__Limnocylindrales;f__Limnocylindraceae;g__Limnocylindrus	95.0	97.90	97.90	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2023-06-05 18:03:37,448] [INFO] GTDB search result was written to GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/result_gtdb.tsv
[2023-06-05 18:03:37,449] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:03:37,463] [INFO] DFAST_QC result json was written to GCA_902754555.1_SRR3727516_bin75_mag_fasta_genomic.fna/dqc_result.json
[2023-06-05 18:03:37,463] [INFO] DFAST_QC completed!
[2023-06-05 18:03:37,463] [INFO] Total running time: 0h0m42s