[2023-06-04 22:02:39,521] [INFO] DFAST_QC pipeline started.
[2023-06-04 22:02:39,524] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 22:02:39,524] [INFO] DQC Reference Directory: /var/lib/cwl/stg0971c836-7be8-4f12-85bc-ef23f1cd10e6/dqc_reference
[2023-06-04 22:02:40,809] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 22:02:40,809] [INFO] Task started: Prodigal
[2023-06-04 22:02:40,810] [INFO] Running command: gunzip -c /var/lib/cwl/stg1327691c-4960-4525-9f98-bcf2b0488a8b/GCA_904378045.1_Chicken_16_mag_12_genomic.fna.gz | prodigal -d GCA_904378045.1_Chicken_16_mag_12_genomic.fna/cds.fna -a GCA_904378045.1_Chicken_16_mag_12_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 22:02:45,279] [INFO] Task succeeded: Prodigal
[2023-06-04 22:02:45,280] [INFO] Task started: HMMsearch
[2023-06-04 22:02:45,280] [INFO] Running command: hmmsearch --tblout GCA_904378045.1_Chicken_16_mag_12_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0971c836-7be8-4f12-85bc-ef23f1cd10e6/dqc_reference/reference_markers.hmm GCA_904378045.1_Chicken_16_mag_12_genomic.fna/protein.faa > /dev/null
[2023-06-04 22:02:45,513] [INFO] Task succeeded: HMMsearch
[2023-06-04 22:02:45,515] [INFO] Found 6/6 markers.
[2023-06-04 22:02:45,548] [INFO] Query marker FASTA was written to GCA_904378045.1_Chicken_16_mag_12_genomic.fna/markers.fasta
[2023-06-04 22:02:45,549] [INFO] Task started: Blastn
[2023-06-04 22:02:45,549] [INFO] Running command: blastn -query GCA_904378045.1_Chicken_16_mag_12_genomic.fna/markers.fasta -db /var/lib/cwl/stg0971c836-7be8-4f12-85bc-ef23f1cd10e6/dqc_reference/reference_markers.fasta -out GCA_904378045.1_Chicken_16_mag_12_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:02:46,114] [INFO] Task succeeded: Blastn
[2023-06-04 22:02:46,119] [INFO] Selected 23 target genomes.
[2023-06-04 22:02:46,120] [INFO] Target genome list was writen to GCA_904378045.1_Chicken_16_mag_12_genomic.fna/target_genomes.txt
[2023-06-04 22:02:46,124] [INFO] Task started: fastANI
[2023-06-04 22:02:46,124] [INFO] Running command: fastANI --query /var/lib/cwl/stg1327691c-4960-4525-9f98-bcf2b0488a8b/GCA_904378045.1_Chicken_16_mag_12_genomic.fna.gz --refList GCA_904378045.1_Chicken_16_mag_12_genomic.fna/target_genomes.txt --output GCA_904378045.1_Chicken_16_mag_12_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 22:02:59,488] [INFO] Task succeeded: fastANI
[2023-06-04 22:02:59,489] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0971c836-7be8-4f12-85bc-ef23f1cd10e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 22:02:59,490] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0971c836-7be8-4f12-85bc-ef23f1cd10e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 22:02:59,492] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 22:02:59,492] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-04 22:02:59,492] [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
--------------------------------------------------------------------------------
[2023-06-04 22:02:59,494] [INFO] DFAST Taxonomy check result was written to GCA_904378045.1_Chicken_16_mag_12_genomic.fna/tc_result.tsv
[2023-06-04 22:02:59,495] [INFO] ===== Taxonomy check completed =====
[2023-06-04 22:02:59,495] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 22:02:59,496] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0971c836-7be8-4f12-85bc-ef23f1cd10e6/dqc_reference/checkm_data
[2023-06-04 22:02:59,500] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 22:02:59,525] [INFO] Task started: CheckM
[2023-06-04 22:02:59,525] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_904378045.1_Chicken_16_mag_12_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_904378045.1_Chicken_16_mag_12_genomic.fna/checkm_input GCA_904378045.1_Chicken_16_mag_12_genomic.fna/checkm_result
[2023-06-04 22:03:20,071] [INFO] Task succeeded: CheckM
[2023-06-04 22:03:20,072] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.62%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 22:03:20,092] [INFO] ===== Completeness check finished =====
[2023-06-04 22:03:20,093] [INFO] ===== Start GTDB Search =====
[2023-06-04 22:03:20,093] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_904378045.1_Chicken_16_mag_12_genomic.fna/markers.fasta)
[2023-06-04 22:03:20,093] [INFO] Task started: Blastn
[2023-06-04 22:03:20,093] [INFO] Running command: blastn -query GCA_904378045.1_Chicken_16_mag_12_genomic.fna/markers.fasta -db /var/lib/cwl/stg0971c836-7be8-4f12-85bc-ef23f1cd10e6/dqc_reference/reference_markers_gtdb.fasta -out GCA_904378045.1_Chicken_16_mag_12_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 22:03:20,865] [INFO] Task succeeded: Blastn
[2023-06-04 22:03:20,870] [INFO] Selected 28 target genomes.
[2023-06-04 22:03:20,870] [INFO] Target genome list was writen to GCA_904378045.1_Chicken_16_mag_12_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 22:03:21,066] [INFO] Task started: fastANI
[2023-06-04 22:03:21,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg1327691c-4960-4525-9f98-bcf2b0488a8b/GCA_904378045.1_Chicken_16_mag_12_genomic.fna.gz --refList GCA_904378045.1_Chicken_16_mag_12_genomic.fna/target_genomes_gtdb.txt --output GCA_904378045.1_Chicken_16_mag_12_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 22:03:32,389] [INFO] Task succeeded: fastANI
[2023-06-04 22:03:32,399] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 22:03:32,399] [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_904378045.1	s__Metalachnospira gallinarum	100.0	647	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Metalachnospira	95.0	98.89	98.22	0.91	0.87	4	conclusive
GCA_902406135.1	s__Metalachnospira sp902406135	80.3132	252	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Metalachnospira	95.0	97.90	97.90	0.93	0.93	2	-
GCF_018918145.1	s__Metalachnospira sp900553995	78.2492	137	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Metalachnospira	95.0	97.83	97.77	0.91	0.89	4	-
GCA_900548595.1	s__Metalachnospira sp900548595	78.2304	149	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Metalachnospira	95.0	98.61	98.00	0.86	0.73	5	-
GCA_900546215.1	s__Metalachnospira sp900546215	77.6561	176	651	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Anaerotignaceae;g__Metalachnospira	95.0	99.21	98.14	0.83	0.82	4	-
--------------------------------------------------------------------------------
[2023-06-04 22:03:32,401] [INFO] GTDB search result was written to GCA_904378045.1_Chicken_16_mag_12_genomic.fna/result_gtdb.tsv
[2023-06-04 22:03:32,401] [INFO] ===== GTDB Search completed =====
[2023-06-04 22:03:32,404] [INFO] DFAST_QC result json was written to GCA_904378045.1_Chicken_16_mag_12_genomic.fna/dqc_result.json
[2023-06-04 22:03:32,404] [INFO] DFAST_QC completed!
[2023-06-04 22:03:32,404] [INFO] Total running time: 0h0m53s