[2023-06-29 21:28:13,692] [INFO] DFAST_QC pipeline started.
[2023-06-29 21:28:13,694] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 21:28:13,694] [INFO] DQC Reference Directory: /var/lib/cwl/stgef05ada8-5b72-46bb-93a9-ca6fd5914942/dqc_reference
[2023-06-29 21:28:15,013] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 21:28:15,014] [INFO] Task started: Prodigal
[2023-06-29 21:28:15,014] [INFO] Running command: gunzip -c /var/lib/cwl/stg27cf2ee5-06b0-489c-b2e6-870f812f0d1a/GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna.gz | prodigal -d GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/cds.fna -a GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 21:28:17,756] [INFO] Task succeeded: Prodigal
[2023-06-29 21:28:17,756] [INFO] Task started: HMMsearch
[2023-06-29 21:28:17,756] [INFO] Running command: hmmsearch --tblout GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef05ada8-5b72-46bb-93a9-ca6fd5914942/dqc_reference/reference_markers.hmm GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/protein.faa > /dev/null
[2023-06-29 21:28:17,980] [INFO] Task succeeded: HMMsearch
[2023-06-29 21:28:17,982] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg27cf2ee5-06b0-489c-b2e6-870f812f0d1a/GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna.gz]
[2023-06-29 21:28:17,998] [INFO] Query marker FASTA was written to GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/markers.fasta
[2023-06-29 21:28:17,999] [INFO] Task started: Blastn
[2023-06-29 21:28:17,999] [INFO] Running command: blastn -query GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/markers.fasta -db /var/lib/cwl/stgef05ada8-5b72-46bb-93a9-ca6fd5914942/dqc_reference/reference_markers.fasta -out GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:28:18,628] [INFO] Task succeeded: Blastn
[2023-06-29 21:28:18,635] [INFO] Selected 25 target genomes.
[2023-06-29 21:28:18,636] [INFO] Target genome list was writen to GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/target_genomes.txt
[2023-06-29 21:28:18,689] [INFO] Task started: fastANI
[2023-06-29 21:28:18,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg27cf2ee5-06b0-489c-b2e6-870f812f0d1a/GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna.gz --refList GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/target_genomes.txt --output GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 21:28:31,138] [INFO] Task succeeded: fastANI
[2023-06-29 21:28:31,138] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef05ada8-5b72-46bb-93a9-ca6fd5914942/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 21:28:31,139] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef05ada8-5b72-46bb-93a9-ca6fd5914942/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 21:28:31,141] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 21:28:31,141] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 21:28:31,141] [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
--------------------------------------------------------------------------------
[2023-06-29 21:28:31,146] [INFO] DFAST Taxonomy check result was written to GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/tc_result.tsv
[2023-06-29 21:28:31,146] [INFO] ===== Taxonomy check completed =====
[2023-06-29 21:28:31,146] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 21:28:31,147] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef05ada8-5b72-46bb-93a9-ca6fd5914942/dqc_reference/checkm_data
[2023-06-29 21:28:31,150] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 21:28:31,168] [INFO] Task started: CheckM
[2023-06-29 21:28:31,168] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/checkm_input GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/checkm_result
[2023-06-29 21:28:48,260] [INFO] Task succeeded: CheckM
[2023-06-29 21:28:48,261] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 21:28:48,285] [INFO] ===== Completeness check finished =====
[2023-06-29 21:28:48,286] [INFO] ===== Start GTDB Search =====
[2023-06-29 21:28:48,286] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/markers.fasta)
[2023-06-29 21:28:48,287] [INFO] Task started: Blastn
[2023-06-29 21:28:48,287] [INFO] Running command: blastn -query GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/markers.fasta -db /var/lib/cwl/stgef05ada8-5b72-46bb-93a9-ca6fd5914942/dqc_reference/reference_markers_gtdb.fasta -out GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 21:28:49,227] [INFO] Task succeeded: Blastn
[2023-06-29 21:28:49,233] [INFO] Selected 16 target genomes.
[2023-06-29 21:28:49,233] [INFO] Target genome list was writen to GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 21:28:49,238] [INFO] Task started: fastANI
[2023-06-29 21:28:49,239] [INFO] Running command: fastANI --query /var/lib/cwl/stg27cf2ee5-06b0-489c-b2e6-870f812f0d1a/GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna.gz --refList GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/target_genomes_gtdb.txt --output GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 21:28:52,973] [INFO] Task succeeded: fastANI
[2023-06-29 21:28:52,986] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 21:28:52,986] [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_903836945.1	s__AAA044-D11 sp903836945	99.7604	351	382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.73	99.63	0.93	0.90	11	conclusive
GCA_000485495.1	s__AAA044-D11 sp000485495	78.4587	97	382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903871555.1	s__AAA044-D11 sp903871555	78.391	125	382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.45	99.05	0.90	0.84	22	-
GCA_903822245.1	s__AAA044-D11 sp903822245	78.2348	112	382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_007280395.1	s__AAA044-D11 sp007280395	78.1161	82	382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842675.1	s__AAA044-D11 sp903842675	78.046	115	382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	98.43	97.97	0.83	0.78	19	-
GCA_009726125.1	s__AAA044-D11 sp009726125	77.6929	121	382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	99.98	99.96	0.97	0.96	6	-
GCA_009701575.1	s__AAA044-D11 sp009701575	77.6531	100	382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002367715.1	s__AAA044-D11 sp002367715	77.3864	91	382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	98.65	98.65	0.87	0.87	2	-
GCA_009701525.1	s__AAA044-D11 sp009701525	77.2738	91	382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903838295.1	s__PALSA-747 sp903838295	77.074	54	382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.94	99.80	0.98	0.95	27	-
GCA_009705075.1	s__AAA044-D11 sp009705075	76.3828	65	382	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__AAA044-D11	95.0	98.34	98.34	0.77	0.77	2	-
--------------------------------------------------------------------------------
[2023-06-29 21:28:52,988] [INFO] GTDB search result was written to GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/result_gtdb.tsv
[2023-06-29 21:28:52,989] [INFO] ===== GTDB Search completed =====
[2023-06-29 21:28:52,992] [INFO] DFAST_QC result json was written to GCA_903835545.1_freshwater_MAG_---_MJ-2014-D1_bin-0792_genomic.fna/dqc_result.json
[2023-06-29 21:28:52,992] [INFO] DFAST_QC completed!
[2023-06-29 21:28:52,992] [INFO] Total running time: 0h0m39s