[2023-06-19 06:45:24,775] [INFO] DFAST_QC pipeline started.
[2023-06-19 06:45:24,781] [INFO] DFAST_QC version: 0.5.7
[2023-06-19 06:45:24,782] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf2c7399-1909-499e-ab0a-b71fae198df8/dqc_reference
[2023-06-19 06:45:26,189] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-19 06:45:26,190] [INFO] Task started: Prodigal
[2023-06-19 06:45:26,190] [INFO] Running command: gunzip -c /var/lib/cwl/stgfc0b9974-a76e-46fc-9d2a-e13dcbbc8625/GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-19 06:45:38,596] [INFO] Task succeeded: Prodigal
[2023-06-19 06:45:38,596] [INFO] Task started: HMMsearch
[2023-06-19 06:45:38,597] [INFO] Running command: hmmsearch --tblout GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf2c7399-1909-499e-ab0a-b71fae198df8/dqc_reference/reference_markers.hmm GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-19 06:45:38,846] [INFO] Task succeeded: HMMsearch
[2023-06-19 06:45:38,848] [INFO] Found 6/6 markers.
[2023-06-19 06:45:38,879] [INFO] Query marker FASTA was written to GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-19 06:45:38,880] [INFO] Task started: Blastn
[2023-06-19 06:45:38,880] [INFO] Running command: blastn -query GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf2c7399-1909-499e-ab0a-b71fae198df8/dqc_reference/reference_markers.fasta -out GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:45:39,476] [INFO] Task succeeded: Blastn
[2023-06-19 06:45:39,480] [INFO] Selected 35 target genomes.
[2023-06-19 06:45:39,480] [INFO] Target genome list was writen to GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-19 06:45:39,487] [INFO] Task started: fastANI
[2023-06-19 06:45:39,487] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc0b9974-a76e-46fc-9d2a-e13dcbbc8625/GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-19 06:45:59,968] [INFO] Task succeeded: fastANI
[2023-06-19 06:45:59,969] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf2c7399-1909-499e-ab0a-b71fae198df8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-19 06:45:59,969] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf2c7399-1909-499e-ab0a-b71fae198df8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-19 06:45:59,971] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-19 06:45:59,972] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-19 06:45:59,972] [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
--------------------------------------------------------------------------------
[2023-06-19 06:45:59,974] [INFO] DFAST Taxonomy check result was written to GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-19 06:45:59,975] [INFO] ===== Taxonomy check completed =====
[2023-06-19 06:45:59,975] [INFO] ===== Start completeness check using CheckM =====
[2023-06-19 06:45:59,975] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf2c7399-1909-499e-ab0a-b71fae198df8/dqc_reference/checkm_data
[2023-06-19 06:45:59,980] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-19 06:46:00,013] [INFO] Task started: CheckM
[2023-06-19 06:46:00,013] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-19 06:46:40,370] [INFO] Task succeeded: CheckM
[2023-06-19 06:46:40,372] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-19 06:46:40,397] [INFO] ===== Completeness check finished =====
[2023-06-19 06:46:40,397] [INFO] ===== Start GTDB Search =====
[2023-06-19 06:46:40,398] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-19 06:46:40,398] [INFO] Task started: Blastn
[2023-06-19 06:46:40,398] [INFO] Running command: blastn -query GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf2c7399-1909-499e-ab0a-b71fae198df8/dqc_reference/reference_markers_gtdb.fasta -out GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-19 06:46:41,172] [INFO] Task succeeded: Blastn
[2023-06-19 06:46:41,177] [INFO] Selected 15 target genomes.
[2023-06-19 06:46:41,178] [INFO] Target genome list was writen to GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-19 06:46:41,183] [INFO] Task started: fastANI
[2023-06-19 06:46:41,183] [INFO] Running command: fastANI --query /var/lib/cwl/stgfc0b9974-a76e-46fc-9d2a-e13dcbbc8625/GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-19 06:46:47,857] [INFO] Task succeeded: fastANI
[2023-06-19 06:46:47,870] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-19 06:46:47,871] [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_003045825.1	s__UBA10364 sp003045825	98.0809	499	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	98.67	96.47	0.88	0.80	20	conclusive
GCA_905478295.1	s__UBA10364 sp002387615	83.2898	465	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.55	99.11	0.94	0.89	10	-
GCA_002685435.1	s__UBA10364 sp002685435	83.0996	347	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018402665.1	s__UBA10364 sp018402665	83.0655	473	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	96.42	96.42	0.92	0.92	2	-
GCA_003385605.1	s__UBA10364 sp003385605	80.6264	163	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	99.63	99.63	0.71	0.71	2	-
GCA_011525035.1	s__UBA10364 sp011525035	79.8569	150	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003445735.1	s__UBA10364 sp003445735	79.4259	121	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	97.99	97.76	0.85	0.77	3	-
GCA_018623275.1	s__UBA10364 sp018623275	79.0074	94	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905182675.1	s__UBA10364 sp905182675	77.2509	76	779	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Schleiferiaceae;g__UBA10364	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-19 06:46:47,900] [INFO] GTDB search result was written to GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-19 06:46:47,901] [INFO] ===== GTDB Search completed =====
[2023-06-19 06:46:47,906] [INFO] DFAST_QC result json was written to GCA_937889335.1_ERR864073_bin.76_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-19 06:46:47,906] [INFO] DFAST_QC completed!
[2023-06-19 06:46:47,906] [INFO] Total running time: 0h1m23s