[2023-06-29 10:49:48,421] [INFO] DFAST_QC pipeline started.
[2023-06-29 10:49:48,435] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 10:49:48,435] [INFO] DQC Reference Directory: /var/lib/cwl/stga801f4bd-02da-47cd-8f71-7782755cb74f/dqc_reference
[2023-06-29 10:49:50,442] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 10:49:50,443] [INFO] Task started: Prodigal
[2023-06-29 10:49:50,443] [INFO] Running command: gunzip -c /var/lib/cwl/stg5fcfe29d-9a2a-47a8-a65f-3a756169a677/GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna.gz | prodigal -d GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/cds.fna -a GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 10:49:55,886] [INFO] Task succeeded: Prodigal
[2023-06-29 10:49:55,887] [INFO] Task started: HMMsearch
[2023-06-29 10:49:55,887] [INFO] Running command: hmmsearch --tblout GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga801f4bd-02da-47cd-8f71-7782755cb74f/dqc_reference/reference_markers.hmm GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/protein.faa > /dev/null
[2023-06-29 10:49:56,150] [INFO] Task succeeded: HMMsearch
[2023-06-29 10:49:56,151] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg5fcfe29d-9a2a-47a8-a65f-3a756169a677/GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna.gz]
[2023-06-29 10:49:56,179] [INFO] Query marker FASTA was written to GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/markers.fasta
[2023-06-29 10:49:56,179] [INFO] Task started: Blastn
[2023-06-29 10:49:56,180] [INFO] Running command: blastn -query GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga801f4bd-02da-47cd-8f71-7782755cb74f/dqc_reference/reference_markers.fasta -out GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 10:49:56,685] [INFO] Task succeeded: Blastn
[2023-06-29 10:49:56,689] [INFO] Selected 18 target genomes.
[2023-06-29 10:49:56,690] [INFO] Target genome list was writen to GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt
[2023-06-29 10:49:56,694] [INFO] Task started: fastANI
[2023-06-29 10:49:56,694] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fcfe29d-9a2a-47a8-a65f-3a756169a677/GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/target_genomes.txt --output GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 10:50:06,911] [INFO] Task succeeded: fastANI
[2023-06-29 10:50:06,911] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga801f4bd-02da-47cd-8f71-7782755cb74f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 10:50:06,911] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga801f4bd-02da-47cd-8f71-7782755cb74f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 10:50:06,915] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 10:50:06,916] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 10:50:06,916] [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
Enterocloster asparagiformis	strain=DSM 15981	GCA_000158075.1	333367	333367	type	True	76.6554	79	607	95	below_threshold
Enterocloster asparagiformis	strain=DSM 15981	GCA_025149125.1	333367	333367	type	True	76.6047	76	607	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 10:50:06,918] [INFO] DFAST Taxonomy check result was written to GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/tc_result.tsv
[2023-06-29 10:50:06,918] [INFO] ===== Taxonomy check completed =====
[2023-06-29 10:50:06,918] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 10:50:06,918] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga801f4bd-02da-47cd-8f71-7782755cb74f/dqc_reference/checkm_data
[2023-06-29 10:50:06,919] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 10:50:06,946] [INFO] Task started: CheckM
[2023-06-29 10:50:06,947] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/checkm_input GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/checkm_result
[2023-06-29 10:50:28,172] [INFO] Task succeeded: CheckM
[2023-06-29 10:50:28,173] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 45.60%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 10:50:28,191] [INFO] ===== Completeness check finished =====
[2023-06-29 10:50:28,192] [INFO] ===== Start GTDB Search =====
[2023-06-29 10:50:28,192] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/markers.fasta)
[2023-06-29 10:50:28,192] [INFO] Task started: Blastn
[2023-06-29 10:50:28,193] [INFO] Running command: blastn -query GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/markers.fasta -db /var/lib/cwl/stga801f4bd-02da-47cd-8f71-7782755cb74f/dqc_reference/reference_markers_gtdb.fasta -out GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 10:50:28,680] [INFO] Task succeeded: Blastn
[2023-06-29 10:50:28,683] [INFO] Selected 13 target genomes.
[2023-06-29 10:50:28,683] [INFO] Target genome list was writen to GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 10:50:28,692] [INFO] Task started: fastANI
[2023-06-29 10:50:28,692] [INFO] Running command: fastANI --query /var/lib/cwl/stg5fcfe29d-9a2a-47a8-a65f-3a756169a677/GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna.gz --refList GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/target_genomes_gtdb.txt --output GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 10:50:36,854] [INFO] Task succeeded: fastANI
[2023-06-29 10:50:36,863] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 10:50:36,864] [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_910586845.1	s__UBA3402 sp910586845	99.0829	553	607	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_910588865.1	s__UBA3402 sp910588865	79.3705	268	607	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910577935.1	s__UBA3402 sp910577935	78.8543	261	607	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910585645.1	s__UBA3402 sp910585645	78.4981	207	607	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910574345.1	s__UBA3402 sp910574345	78.4911	237	607	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588505.1	s__UBA3402 sp910588505	78.0796	192	607	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__UBA3402	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018715565.1	s__Ventrimonas merdavium	76.7697	80	607	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Ventrimonas	95.0	99.46	99.46	0.97	0.97	2	-
GCA_019114845.1	s__Lachnoclostridium_A stercoripullorum	76.6036	65	607	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Lachnoclostridium_A	95.0	98.44	98.44	0.80	0.80	2	-
GCA_018380885.1	s__Enterocloster sp900555905	76.4917	69	607	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Enterocloster	95.0	98.89	98.89	0.95	0.95	2	-
GCA_017889125.1	s__Caccovicinus sp017889125	76.2199	69	607	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Caccovicinus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 10:50:36,865] [INFO] GTDB search result was written to GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/result_gtdb.tsv
[2023-06-29 10:50:36,866] [INFO] ===== GTDB Search completed =====
[2023-06-29 10:50:36,870] [INFO] DFAST_QC result json was written to GCA_948472565.1_SRR15604638_bin.43_metawrap_v1.3_MAG_genomic.fna/dqc_result.json
[2023-06-29 10:50:36,871] [INFO] DFAST_QC completed!
[2023-06-29 10:50:36,871] [INFO] Total running time: 0h0m48s