[2023-06-29 13:36:31,054] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:36:31,056] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:36:31,056] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fa93a79-fe80-435a-aa5d-2a0bbf0af380/dqc_reference
[2023-06-29 13:36:32,316] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:36:32,317] [INFO] Task started: Prodigal
[2023-06-29 13:36:32,317] [INFO] Running command: gunzip -c /var/lib/cwl/stg571b6781-eea0-4d1a-9e26-87bff2cde50e/GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna.gz | prodigal -d GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/cds.fna -a GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:36:40,900] [INFO] Task succeeded: Prodigal
[2023-06-29 13:36:40,900] [INFO] Task started: HMMsearch
[2023-06-29 13:36:40,900] [INFO] Running command: hmmsearch --tblout GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fa93a79-fe80-435a-aa5d-2a0bbf0af380/dqc_reference/reference_markers.hmm GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:36:41,188] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:36:41,189] [INFO] Found 6/6 markers.
[2023-06-29 13:36:41,221] [INFO] Query marker FASTA was written to GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta
[2023-06-29 13:36:41,222] [INFO] Task started: Blastn
[2023-06-29 13:36:41,222] [INFO] Running command: blastn -query GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fa93a79-fe80-435a-aa5d-2a0bbf0af380/dqc_reference/reference_markers.fasta -out GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:36:41,810] [INFO] Task succeeded: Blastn
[2023-06-29 13:36:41,815] [INFO] Selected 24 target genomes.
[2023-06-29 13:36:41,816] [INFO] Target genome list was writen to GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt
[2023-06-29 13:36:41,822] [INFO] Task started: fastANI
[2023-06-29 13:36:41,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg571b6781-eea0-4d1a-9e26-87bff2cde50e/GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/target_genomes.txt --output GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:36:53,994] [INFO] Task succeeded: fastANI
[2023-06-29 13:36:53,994] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fa93a79-fe80-435a-aa5d-2a0bbf0af380/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:36:53,994] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fa93a79-fe80-435a-aa5d-2a0bbf0af380/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:36:54,000] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:36:54,000] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 13:36:54,000] [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
Fibrobacter succinogenes subsp. succinogenes	strain=S85	GCA_000024665.1	834	833	type	True	79.0202	318	1041	95	below_threshold
Fibrobacter succinogenes subsp. succinogenes	strain=S85	GCA_000146505.1	834	833	type	True	78.9514	319	1041	95	below_threshold
Hallerella succinigenes	strain=UWS3	GCA_002797675.1	1896222	1896222	type	True	78.1303	132	1041	95	below_threshold
Hallerella porci	strain=UWS4	GCA_003148885.1	1945871	1945871	type	True	77.3385	67	1041	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 13:36:54,002] [INFO] DFAST Taxonomy check result was written to GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/tc_result.tsv
[2023-06-29 13:36:54,003] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:36:54,003] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:36:54,003] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fa93a79-fe80-435a-aa5d-2a0bbf0af380/dqc_reference/checkm_data
[2023-06-29 13:36:54,004] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:36:54,053] [INFO] Task started: CheckM
[2023-06-29 13:36:54,053] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/checkm_input GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/checkm_result
[2023-06-29 13:37:26,100] [INFO] Task succeeded: CheckM
[2023-06-29 13:37:26,102] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 17.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:37:26,141] [INFO] ===== Completeness check finished =====
[2023-06-29 13:37:26,142] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:37:26,142] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta)
[2023-06-29 13:37:26,142] [INFO] Task started: Blastn
[2023-06-29 13:37:26,143] [INFO] Running command: blastn -query GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fa93a79-fe80-435a-aa5d-2a0bbf0af380/dqc_reference/reference_markers_gtdb.fasta -out GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:37:26,946] [INFO] Task succeeded: Blastn
[2023-06-29 13:37:26,951] [INFO] Selected 17 target genomes.
[2023-06-29 13:37:26,951] [INFO] Target genome list was writen to GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:37:26,958] [INFO] Task started: fastANI
[2023-06-29 13:37:26,959] [INFO] Running command: fastANI --query /var/lib/cwl/stg571b6781-eea0-4d1a-9e26-87bff2cde50e/GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna.gz --refList GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:37:37,166] [INFO] Task succeeded: fastANI
[2023-06-29 13:37:37,182] [INFO] Found 17 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 13:37:37,183] [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
GCF_003149045.1	s__Fibrobacter sp003149045	83.5875	592	1041	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	99.98	99.98	0.98	0.98	2	-
GCF_900142465.1	s__Fibrobacter sp900142465	83.2929	569	1041	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	98.85	98.41	0.91	0.86	7	-
GCF_900142535.1	s__Fibrobacter sp900142535	82.6899	559	1041	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	96.77	96.77	0.93	0.93	2	-
GCF_002210295.1	s__Fibrobacter sp002210295	79.4636	384	1041	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142475.1	s__Fibrobacter sp900142475	79.4065	354	1041	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	95.25	95.07	0.84	0.80	4	-
GCA_017503015.1	s__Fibrobacter sp017503015	79.0747	278	1041	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002449765.1	s__Fibrobacter sp002449765	79.0616	283	1041	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	98.21	96.54	0.93	0.89	8	-
GCF_002210285.1	s__Fibrobacter sp002210285	79.0555	289	1041	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	96.84	95.65	0.91	0.85	4	-
GCF_900143055.1	s__Fibrobacter sp900143055	78.9975	283	1041	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	96.51	95.61	0.84	0.74	8	-
GCF_900177805.1	s__Fibrobacter sp900177805	78.9524	319	1041	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.22	97.22	0.89	0.89	2	-
GCA_002394865.1	s__Fibrobacter sp002394865	78.9076	294	1041	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	99.99	99.99	0.99	0.99	2	-
GCA_017526585.1	s__Fibrobacter sp017526585	78.8493	288	1041	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017550445.1	s__Fibrobacter sp017550445	78.817	323	1041	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017551775.1	s__Fibrobacter sp017551775	78.7434	291	1041	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002395745.1	s__Fibrobacter sp002395745	78.6516	276	1041	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800815.1	s__Fibrobacter succinogenes_B	78.4577	258	1041	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	97.10	97.10	0.90	0.90	2	-
GCA_017530965.1	s__Fibrobacter sp017530965	78.3583	302	1041	d__Bacteria;p__Fibrobacterota;c__Fibrobacteria;o__Fibrobacterales;f__Fibrobacteraceae;g__Fibrobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:37:37,185] [INFO] GTDB search result was written to GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 13:37:37,185] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:37:37,189] [INFO] DFAST_QC result json was written to GCA_937883935.1_SRR6425756_bin.2_CONCOCT_v1.1_MAG_genomic.fna/dqc_result.json
[2023-06-29 13:37:37,189] [INFO] DFAST_QC completed!
[2023-06-29 13:37:37,189] [INFO] Total running time: 0h1m6s